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PR00504

Identifier
CHROMODOMAIN  [View Relations]  [View Alignment]  
Accession
PR00504
No. of Motifs
3
Creation Date
19-MAY-1996  (UPDATE 23-JUN-1999)
Title
Chromodomain signature
Database References

PROSITE; PS00598 CHROMO_1; PS50013 CHROMO_2
BLOCKS; BL00598
PFAM; PF00385 chromo
INTERPRO; IPR000953
Literature References
1. PARO, R.
Imprinting a determined state into the chromatin of Drosophila.
TRENDS GENET. 6(12) 416-421 (1990).
 
2. SINGH, P.B., MILLER, J.R., PEARCE, J., KOTHARY, R., BURTON, R.D.,
PARO, R., JAMES, T.C. AND GAUNT, S.J.
A sequence motif found in a Drosophila heterochromatin protein is
conserved in animals and plants.
NUCLEIC ACIDS RES. 19(4) 789-794 (1991).
 
3. AASLAND, R. AND STEWART, A.F.
The chrome shadow domain, a second chrome domain in heterochromatin-
binding protein 1, HP1.
NUCLEIC ACIDS RES. 23(16) 3168-3173 (1995).
 
4. KOONIN, E.V., ZHOU, S. AND LUCCHESI, J.C.
The chromo superfamily - new members, duplication of the chromo domain
and possible role in delivering transcription regulators to chromatin.
NUCLEIC ACIDS RES. 23 4229-4233 (1995).

Documentation
The CHROMO (CHRromatin Organization MOdifier) domain [1-4] is a conserved
region of around 60 amino acids, originally identified in Drosophila
modifiers of variegation - these are proteins that alter the structure of
chromatin to the condensed morphology of heterochromatin, a cytologically
visible condition where gene expression is repressed. In one of these
proteins, Polycomb, the chromo domain has been shown to be important for
chromatin targeting. Proteins that contain a chromo domain appear to fall
into 3 classes: (1) those having an N-terminal chromo domain followed by a
region termed the chromo shadow domain [3]; (2) those with a single chromo
domain; and (3) those with paired tandem chromo domains. 
 
CHROMODOMAIN is a 3-element fingerprint that provides a signature for the
chromo domain. The fingerprint was derived from an initial alignment of 7
sequences: the motifs were drawn from short conserved regions spanning the
full domain length, motifs 2 and 3 spanning the region encoded by PROSITE
pattern CHROMO_1 (PS00598). Two iterations on OWL27.1 were required to
reach convergence, at which point a true set comprising 12 sequences was
identified. Several partial matches were also found, all of which are
believed to be family members. This is not a powerful discriminator owing
to the low level of sequence similarity between different chromo domains.
 
An update on SPTR37_9f identified a true set of 30 sequences, and 21
partial matches.
Summary Information
  30 codes involving  3 elements
21 codes involving 2 elements
Composite Feature Index
3303030
241919
123
True Positives
CEC1_CAEEL    HP1A_HUMAN    HP1A_MOUSE    HP1B_HUMAN    
HP1G_HUMAN HP1G_MOUSE HP1_DROME HP1_DROVI
O14600 O17916 O17918 O42934
O49137 O49139 O49141 O49415
O50057 O50073 O55187 O93480
O93481 O93482 PC_DROME Q21370
Q38940 Q91647 Q94996 SUV9_DROME
SWI6_SCHPO YNZ8_CAEEL
True Positive Partials
Codes involving 2 elements
CHD1_HUMAN CHD1_MOUSE CHD1_YEAST CHD2_HUMAN
MOD3_MOUSE O17909 O42142 O42765
O43463 O48579 O54864 O60016
O65791 O74565 Q18313 Q19972
Q19973 Q22430 Q24376 Q25732
YAQ2_SCHPO
Sequence Titles
CEC1_CAEEL  CEC-1 PROTEIN - CAENORHABDITIS ELEGANS.       
HP1A_HUMAN HETEROCHROMATIN PROTEIN 1 HOMOLOG ALPHA (HP1 ALPHA) (ANTIGEN P25) - HOMO SAPIENS (HUMAN).
HP1A_MOUSE HETEROCHROMATIN PROTEIN 1 HOMOLOG ALPHA (HP1 ALPHA) - MUS MUSCULUS (MOUSE).
HP1B_HUMAN HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA (HP1 BETA) (MODIFIER 1 PROTEIN) (M31) (HETEROCHROMATIN PROTEIN P25) - HOMO SAPIENS (HUMAN), AND MUS MUSCULUS (MOUSE).
HP1G_HUMAN HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA (HP1 GAMMA) (MODIFIER 2 PROTEIN) - HOMO SAPIENS (HUMAN).
HP1G_MOUSE HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA (HP1 GAMMA) (MODIFIER 2 PROTEIN) (M32) - MUS MUSCULUS (MOUSE).
HP1_DROME HETEROCHROMATIN PROTEIN 1 (HP1) (NONHISTONE CHROMOSOMAL PROTEIN C1A9 ANTIGEN) - DROSOPHILA MELANOGASTER (FRUIT FLY).
HP1_DROVI HETEROCHROMATIN PROTEIN 1 (HP1) - DROSOPHILA VIRILIS (FRUIT FLY).
O14600 TESTIS-SPECIFIC CHROMODOMAIN Y ISOFORM 1 - HOMO SAPIENS (HUMAN).
O17916 K01G5.2A PROTEIN - CAENORHABDITIS ELEGANS.
O17918 K01G5.2B PROTEIN - CAENORHABDITIS ELEGANS.
O42934 PROBABLE TRANSCRIPTION FACTOR - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
O49137 CHROMOMETHYLASE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O49139 CHROMOMETHYLASE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O49141 CHROMOMETHYLASE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O49415 HYPOTHETICAL 130.9 KD PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O50057 CHROMOMETHYLASE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O50073 CHROMOMETHYLASE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O55187 CHROMOBOX HOMOLOG 4 (DROSOPHILA PC CLASS) (TRANSCRIPTIONAL REPRESSOR MPC2) - MUS MUSCULUS (MOUSE).
O93480 CHROMOBOX PROTEIN (CHCB1) - GALLUS GALLUS (CHICKEN).
O93481 CHROMOBOX PROTEIN (CHCB2) - GALLUS GALLUS (CHICKEN).
O93482 CHROMOBOX PROTEIN (CHCB3) - GALLUS GALLUS (CHICKEN).
PC_DROME POLYCOMB PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q21370 K08H2.6 PROTEIN - CAENORHABDITIS ELEGANS.
Q38940 SIMILARITY TO SWISS-PROT ACCESSION NUMBER P34881 - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
Q91647 XPOLYCOMB - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q94996 PDD1P - TETRAHYMENA THERMOPHILA.
SUV9_DROME SU(VAR)3-9 PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
SWI6_SCHPO SWI6 PROTEIN - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
YNZ8_CAEEL HYPOTHETICAL 37.7 KD PROTEIN T09A5.8 IN CHROMOSOME III - CAENORHABDITIS ELEGANS.

CHD1_HUMAN CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1 (CHD-1) - HOMO SAPIENS (HUMAN).
CHD1_MOUSE CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1 (CHD-1) - MUS MUSCULUS (MOUSE).
CHD1_YEAST CHD1 PROTEIN - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
CHD2_HUMAN CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 2 (CHD-2) - HOMO SAPIENS (HUMAN).
MOD3_MOUSE MODIFIER 3 PROTEIN (M33) - MUS MUSCULUS (MOUSE).
O17909 H06O01.2 PROTEIN - CAENORHABDITIS ELEGANS.
O42142 CHROMO-HELICASE-DNA-BINDING ON THE Z CHROMOSOME PROTEIN - GALLUS GALLUS (CHICKEN).
O42765 ELONGATION-LIKE FACTOR - CANDIDA ALBICANS (YEAST).
O43463 SU(VAR)3-9 HOMOLOG - HOMO SAPIENS (HUMAN).
O48579 HUMAN MI-2 AUTOANTIGEN-LIKE PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O54864 SU(VAR)3-9 HOMOLOG - MUS MUSCULUS (MOUSE).
O60016 CLR4P - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
O65791 POLYCOMB-LIKE PROTEIN - DAUCUS CAROTA (CARROT).
O74565 CLR4 PROTEIN - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
Q18313 COSMID C29H12 - CAENORHABDITIS ELEGANS.
Q19972 SIMILAR TO CHROMO DOMAIN OF HETEROCHROMATIN PROTEIN. NCBI GI: 1118175 - CAENORHABDITIS ELEGANS.
Q19973 CODED FOR BY C. ELEGANS CDNA YK113G4.3 - CAENORHABDITIS ELEGANS.
Q22430 SIMILARITY TO CHROMO DOMAINS - CAENORHABDITIS ELEGANS.
Q24376 CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q25732 CHROMODOMAIN PROTEIN - PLASMODIUM FALCIPARUM.
YAQ2_SCHPO HYPOTHETICAL 108.7 KD PROTEIN C18G6.02C IN CHROMOSOME I - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
Scan History
OWL27_1    2  200  NSINGLE    
SPTR37_9f 4 400 NSINGLE
Initial Motifs
Motif 1  width=9
Element Seqn Id St Int Rpt
EEEYVVEKV MOD1_MOUSE 18 18 -
EEGKVLEKT YEZ4_YEAST 192 192 -
EEEYAVEKI HP1_DROME 21 21 -
DLVYAAEKI PC_DROME 23 23 -
EDEYVVEKV SWI6_SCHPO 78 78 -
DEIFEVEKI YNZ8_CAEEL 21 21 -
KGEYVVERI SUV9_DROME 216 216 -

Motif 2 width=15
Element Seqn Id St Int Rpt
VTDNLLVLQVRWLGY YNZ8_CAEEL 34 4 -
MDQYQPVFFVKWLGY SUV9_DROME 229 4 -
VVKGKVEYLLKWKGF MOD1_MOUSE 31 4 -
NCKENYEFLIKWTDE YEZ4_YEAST 206 5 -
VRKGKVEYYLKWKGY HP1_DROME 34 4 -
VKKGVVEYRVKWKGW PC_DROME 36 4 -
RKGGGYEYLLKWEGY SWI6_SCHPO 93 6 -

Motif 3 width=13
Element Seqn Id St Int Rpt
PETENTWEPENNL HP1_DROME 49 0 -
DPSDNTWSSEADC SWI6_SCHPO 109 1 -
GADEDTWEPEEDL YNZ8_CAEEL 49 0 -
HDSENTWESLANV SUV9_DROME 244 0 -
SDEDNTWEPEENL MOD1_MOUSE 46 0 -
SHLHNTWETYESI YEZ4_YEAST 221 0 -
NQRYNTWEPEVNI PC_DROME 51 0 -
Final Motifs
Motif 1  width=9
Element Seqn Id St Int Rpt
EEEYVVEKV HP1B_HUMAN 18 18 -
EEEYVVEKV O93480 18 18 -
PEEFVVEKV O93481 17 17 -
PEEFVVEKV HP1G_MOUSE 17 17 -
PEEFVVEKV HP1G_HUMAN 17 17 -
EEEYVVEKV HP1A_HUMAN 17 17 -
EEEYVVEKV HP1A_MOUSE 17 17 -
EEEYAVEKI HP1_DROME 21 21 -
EEEYAVEKI HP1_DROVI 21 21 -
EHVFAVESI Q91647 8 8 -
EHVFAVESI O55187 8 8 -
EHVFAVESI O93482 8 8 -
PGEFEVEKF O49137 336 336 -
PGEFEVEKF Q38940 254 254 -
PGEFEVEKF O50073 336 336 -
PGEFEVEKF O50057 336 336 -
PGEFEVEKF O49141 336 336 -
PGEFEVEKF O49139 336 336 -
DLVYAAEKI PC_DROME 23 23 -
SQEFEVEAI O14600 3 3 -
SNVFVVEKV Q21370 34 34 -
EDEYVVEKV SWI6_SCHPO 78 78 -
DEIFEVEKI YNZ8_CAEEL 21 21 -
DNVFMVEKV O17916 16 16 -
DNVFMVEKV O17918 16 16 -
EDQYEVEKI Q94996 46 46 -
SEEYEVEKL O49415 783 783 -
SELYTVESI CEC1_CAEEL 5 5 -
DEEFAVEMI O42934 173 173 -
KGEYVVERI SUV9_DROME 216 216 -

Motif 2 width=15
Element Seqn Id St Int Rpt
VVKGKVEYLLKWKGF HP1B_HUMAN 31 4 -
VVKGKVEYLLKWKGF O93480 31 4 -
VVNGKVEYYLKWKGF O93481 30 4 -
VVNGKVEYFLKWKGF HP1G_MOUSE 30 4 -
VVNGKVEYFLKWKGF HP1G_HUMAN 30 4 -
VVKGQVEYLLKWKGF HP1A_HUMAN 30 4 -
MVKGQVEYLLKWKGF HP1A_MOUSE 30 4 -
VRKGKVEYYLKWKGY HP1_DROME 34 4 -
VRKGKVEYYLKWKGY HP1_DROVI 34 4 -
IRKGRVEYLVKWRGW Q91647 21 4 -
IRKGRVEYLVKWRGW O55187 21 4 -
IRKGRVEYLVKWRGW O93482 21 4 -
TGEKTLQLMVRWKGY O49137 355 10 -
TGEKTLQLMVRWKGY Q38940 273 10 -
TGEKTLQLMVRWKGY O50073 355 10 -
TGEKTLQLMVRWKGY O50057 355 10 -
TGEKTLQLMVRWKGY O49141 355 10 -
TGEKTLQLMVRWKGY O49139 355 10 -
VKKGVVEYRVKWKGW PC_DROME 36 4 -
DKNGNTQYLVRWKGY O14600 17 5 -
LTRGGSEYYIKWQGF Q21370 47 4 -
RKGGGYEYLLKWEGY SWI6_SCHPO 93 6 -
VTDNLLVLQVRWLGY YNZ8_CAEEL 34 4 -
GKAGRDEFLIQWQGF O17916 30 5 -
GKAGRDEFLIQWQGF O17918 30 5 -
PKTKQKEYLVKWENW Q94996 61 6 -
TGKNGLKFKVHWKGY O49415 802 10 -
KKKGKSEFYIKWLGY CEC1_CAEEL 18 4 -
KDGSGFQYYLKWEGY O42934 188 6 -
MDQYQPVFFVKWLGY SUV9_DROME 229 4 -

Motif 3 width=13
Element Seqn Id St Int Rpt
SDEDNTWEPEENL HP1B_HUMAN 46 0 -
SDEDNTWEPEENL O93480 46 0 -
TDADNTWEPEENL O93481 45 0 -
TDADNTWEPEENL HP1G_MOUSE 45 0 -
TDADNTWEPEENL HP1G_HUMAN 45 0 -
SEEHNTWEPEKNL HP1A_HUMAN 45 0 -
SEEHNTWEPEKNL HP1A_MOUSE 45 0 -
PETENTWEPENNL HP1_DROME 49 0 -
AETENTWEPEGNL HP1_DROVI 49 0 -
SSKYNTWEPEENI Q91647 36 0 -
SPKYNTWEPEENI O55187 36 0 -
SPKYNTWEPEENI O93482 36 0 -
NSSYDTWEPYSGL O49137 370 0 -
NSSYDTWEPYSGL Q38940 288 0 -
NSSYDTWEPYSGL O50073 370 0 -
NSSYDTWEPYSGL O50057 370 0 -
NSSYDTWEPYSGL O49141 370 0 -
NSSYDTWEPYSGL O49139 370 0 -
NQRYNTWEPEVNI PC_DROME 51 0 -
DKQDDTWEPEQHL O14600 32 0 -
PESECSWEPIENL Q21370 62 0 -
DPSDNTWSSEADC SWI6_SCHPO 109 1 -
GADEDTWEPEEDL YNZ8_CAEEL 49 0 -
PESDSSWEPRENL O17916 45 0 -
PESDSSWEPRENL O17918 45 0 -
PIEDSTWEPYEHL Q94996 76 0 -
RSDEDTWELAEEL O49415 817 0 -
DHTHNSWEPKENI CEC1_CAEEL 33 0 -
DPSDNTWNDEEDC O42934 204 1 -
HDSENTWESLANV SUV9_DROME 244 0 -