SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR00882

Identifier
RIBOSOMALL7A  [View Relations]  [View Alignment]  
Accession
PR00882
No. of Motifs
7
Creation Date
08-JUN-1998  (UPDATE 07-JUN-1999)
Title
Ribosomal protein L7A family signature
Database References
PRINTS; PR00881 L7ARS6FAMILY
PFAM; PF01248 Ribosomal_L7Ae
INTERPRO; IPR001921
Literature References
1. COLOMBO, P., YON J. AND FRIED, M.
The organization and expression of the human L7a ribosomal protein gene. 
BIOCHIM.BIOPHYS.ACTA 1129 93-95 (1991). 
 
2. AREVALO, S.G. AND WARNER, J.R.
Ribosomal protein L4 of Saccharomyces cerevisiae: the gene and its protein. 
NUCLEIC ACIDS RES. 18 1447-1449 (1990). 
 
3. YON, J., GIALLONGO, A. AND FRIED, M.
The organization and expression of the Saccharomyces cerevisiae L4 ribosomal
protein genes and their identification as the homologues of the mammalian
ribosomal protein gene L7a. 
MOL.GEN.GENET. 227 72-80 (1991). 
 
4. KOLODRUBETZ, D. AND BURGUM, A.
Sequence and genetic-analysis of NHP2 - a moderately abundant high 
mobility group-like nuclear-protein with an essential function in
Saccharomyces cerevisiae.
YEAST 7(2) 79-90 (1991).

Documentation
The genomic structure and sequence of the human ribosomal protein L7a has
been determined [1]. The gene contains 8 exons and 7 introns, encompassing
3179 bp. The human gene resembles other mammalian ribosomal protein genes
in so far as it contains a short first exon, a short 5' untranslated leader
and its transcriptional start sites at C residues embedded in a poly-
pyrimidine tract [1].
 
The sequence of a gene for ribosomal protein L4 of S.cerevisiae has also 
been determined, which, unlike most of its other ribosomal protein genes,
has no intron [2]. The single open reading frame is highly similar to
mammalian ribosomal protein L7a. 
 
There appear to be two genes for L4, both of which are active [2]. Yeast
cells containing a disruption of the L4-1 gene form smaller colonies than
either wild-type or disrupted L4-2 strains. Disruption of both L4 genes is
lethal, probably resulting from an inability of the organism to produce
functional ribosomes. [3]
 
Several other ribosomal proteins have been found to share sequence 
similarity with L7a, including yeast NHP2 [4], B.subtilis hypothetical 
protein ylxQ, Halobacterium marismortui Hs6, and M.jannaschii MJ1203.
 
RIBOSOMALL7A is a 7-element fingerprint that provides a signature for
the L7A family of ribosomal proteins. The fingerprint was derived from
an initial alignment of 4 sequences: the motifs were drawn from short
conserved sections spanning virtually the full alignment length, focusing
on those regions that characterise the ribosomal L7A proteins but
distinguish them from the rest of the HMG-like family. Two iterations
on OWL30.2 were required to reach convergence, at which point a true
set comprising 14 sequences was identified. Two partial matches were
also found, both of which are fragments: RL7A_ARATH is an Arabidopsis L7A 
protein that matches motifs 1-5; and SSO4A09 is a porcine L7A protein
that matches motifs 4-6.
 
An update on SPTR37_9f identified a true set of 11 sequences.
Summary Information
11 codes involving  7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
711111111111111
60000000
50000000
40000000
30000000
20000000
1234567
True Positives
RL7A_ANOGA    RL7A_ARATH    RL7A_CHICK    RL7A_DROME    
RL7A_FUGRU RL7A_HUMAN RL7A_MOUSE RL7A_ORYSA
RL8A_YEAST RL8B_YEAST RL8_SCHPO
Sequence Titles
RL7A_ANOGA  60S RIBOSOMAL PROTEIN L7A - ANOPHELES GAMBIAE (AFRICAN MALARIA MOSQUITO). 
RL7A_ARATH 60S RIBOSOMAL PROTEIN L7A - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
RL7A_CHICK 60S RIBOSOMAL PROTEIN L7A - GALLUS GALLUS (CHICKEN).
RL7A_DROME 60S RIBOSOMAL PROTEIN L7A - DROSOPHILA MELANOGASTER (FRUIT FLY).
RL7A_FUGRU 60S RIBOSOMAL PROTEIN L7A - FUGU RUBRIPES (JAPANESE PUFFERFISH) (TAKIFUGU RUBRIPES).
RL7A_HUMAN 60S RIBOSOMAL PROTEIN L7A (PLA-X POLYPEPTIDE) (SURF-3) - HOMO SAPIENS (HUMAN), AND RATTUS NORVEGICUS (RAT).
RL7A_MOUSE 60S RIBOSOMAL PROTEIN L7A (SURFEIT LOCUS PROTEIN 3) - MUS MUSCULUS (MOUSE).
RL7A_ORYSA 60S RIBOSOMAL PROTEIN L7A - ORYZA SATIVA (RICE).
RL8A_YEAST 60S RIBOSOMAL PROTEIN L8-A (L7A-2) (L4-2) (YL5) (RP6) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
RL8B_YEAST 60S RIBOSOMAL PROTEIN L8-B (L7A-1) (L4-1) (YL5) (RP6) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
RL8_SCHPO 60S RIBOSOMAL PROTEIN L8 (L7A) (L4) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
Scan History
OWL30_2    2  50   NSINGLE    
SPTR37_9f 2 12 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
PKNFGIGQAVQPKRNLSR P10664 30 30 -
PKNFGIGQAVQPKRNLSR P49626 30 30 -
PKNFGIGQDIQPKRDLTR RL7A_MOUSE 35 35 -
PKNFGIGQNVQPKRDLSR RL7A_DROME 41 41 -

Motif 2 width=18
Element Seqn Id St Int Rpt
RYVKWPEYVRLQRQKKIL P49626 47 -1 -
RFVKWPRYIRLQRQRAIL RL7A_MOUSE 52 -1 -
RFVRWPKYIRVQRQKAVL RL7A_DROME 58 -1 -
RYVKWPEYVRVQRQKKIL P10664 47 -1 -

Motif 3 width=20
Element Seqn Id St Int Rpt
RLKVPPTIAQFQYTLDRNTA P10664 67 2 -
RLKVPPTIAQFQYTLDRNTA P49626 67 2 -
RLKVPPPIHQFSQTLDKTTA RL7A_DROME 78 2 -
RLKVPPAINQFTQALDRQTA RL7A_MOUSE 72 2 -

Motif 4 width=14
Element Seqn Id St Int Rpt
KLFNKYRPETAAEK P49626 91 4 -
KLAHKYRPETKQEK RL7A_MOUSE 96 4 -
KLLEKYRPESALAK RL7A_DROME 102 4 -
KLFNKYRPETAAEK P10664 91 4 -

Motif 5 width=21
Element Seqn Id St Int Rpt
KPYAVKYGLNHVVSLIENKKA P49626 127 22 -
KPYAVKYGLNHVVALIENKKA P10664 127 22 -
RPPVLRAGVNTVTTLVENKKA RL7A_MOUSE 131 21 -
KPSYVSAGTNTVTKLIEQKKA RL7A_DROME 137 21 -

Motif 6 width=25
Element Seqn Id St Int Rpt
LVRRKTCTTLALTTVDNNDKANFGK RL7A_DROME 198 40 -
LVNQKTSAVAALTEVRAEDEAALAK P49626 188 40 -
LVNQKTSAVAALTEVRAEDEAALAK P10664 188 40 -
LVHRKTCTTVAFTQVNSEDKGALAK RL7A_MOUSE 192 40 -

Motif 7 width=21
Element Seqn Id St Int Rpt
NFNERHEEIRRHWGGGILGSK RL7A_DROME 230 7 -
NFADKYDEVKKHWGGGILGNK P49626 220 7 -
NYNDRYDEIRRHWGGNVLGPK RL7A_MOUSE 224 7 -
NFADKYDEVKKHWGGGILGNK P10664 220 7 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
PKNFGIGQDIQPKRDLTR RL7A_HUMAN 35 35 -
PKNFGIGQDIQPKRDLTR RL7A_MOUSE 35 35 -
PKNFGIGQDIQPKRDLTR RL7A_CHICK 35 35 -
PKNFGIGQDIQPKRDLTR RL7A_FUGRU 35 35 -
PKNFGIGQAVQPKRNLSR RL8B_YEAST 30 30 -
PKNFGIGQAVQPKRNLSR RL8A_YEAST 30 30 -
PRSFGIGQDIQPKRDLSR RL8_SCHPO 30 30 -
PKNFGIGQNVQPKRDLSR RL7A_DROME 41 41 -
PKQFGIGGALPPKKDLSR RL7A_ARATH 28 28 -
PKQFGIGGALPPKKDLHR RL7A_ORYSA 29 29 -
VKNYGIGQNVQPKRDLSR RL7A_ANOGA 42 42 -

Motif 2 width=18
Element Seqn Id St Int Rpt
RFVKWPRYIRLQRQRAIL RL7A_HUMAN 52 -1 -
RFVKWPRYIRLQRQRAIL RL7A_MOUSE 52 -1 -
RFVKWPRYIRLQRQRSIL RL7A_CHICK 52 -1 -
RFVKWPRYIRLQRQRSIL RL7A_FUGRU 52 -1 -
RYVKWPEYVRLQRQKKIL RL8B_YEAST 47 -1 -
RYVKWPEYVRVQRQKKIL RL8A_YEAST 47 -1 -
RFVKWPEYIRLQRRRKIL RL8_SCHPO 47 -1 -
RFVRWPKYIRVQRQKAVL RL7A_DROME 58 -1 -
RYIKWPKSIRLQRQKRIL RL7A_ARATH 45 -1 -
RFVKWPKVVRIQRQRRIL RL7A_ORYSA 46 -1 -
RFVKWPKYIRIQRHRAIL RL7A_ANOGA 59 -1 -

Motif 3 width=20
Element Seqn Id St Int Rpt
RLKVPPAINQFTQALDRQTA RL7A_HUMAN 72 2 -
RLKVPPAINQFTQALDRQTA RL7A_MOUSE 72 2 -
RLKVPPAINQFSQALDRQTA RL7A_CHICK 72 2 -
RLKVPPAINQFTQALDRQTA RL7A_FUGRU 72 2 -
RLKVPPTIAQFQYTLDRNTA RL8B_YEAST 67 2 -
RLKVPPTIAQFQYTLDRNTA RL8A_YEAST 67 2 -
RLKVPPAIAQFQKTLDKNTA RL8_SCHPO 67 2 -
RLKVPPPIHQFSQTLDKTTA RL7A_DROME 78 2 -
RLKVPPALNQFTKTLDKNLA RL7A_ARATH 65 2 -
RLKVPPALNQFTRTLDKNLA RL7A_ORYSA 66 2 -
RLKIPPPINQFTQTLDKPTA RL7A_ANOGA 79 2 -

Motif 4 width=14
Element Seqn Id St Int Rpt
KLAHKYRPETKQEK RL7A_HUMAN 96 4 -
KLAHKYRPETKQEK RL7A_MOUSE 96 4 -
KLAHKYRPETKQEK RL7A_CHICK 96 4 -
KLAHKYRPETKQEK RL7A_FUGRU 96 4 -
KLFNKYRPETAAEK RL8B_YEAST 91 4 -
KLFNKYRPETAAEK RL8A_YEAST 91 4 -
KLLNKYRPETAAEK RL8_SCHPO 91 4 -
KLLEKYRPESALAK RL7A_DROME 102 4 -
KVLLKYRPEDKAAK RL7A_ARATH 89 4 -
KMLLKYRPEDKAAK RL7A_ORYSA 90 4 -
KCWKKYRPENPIAR RL7A_ANOGA 103 4 -

Motif 5 width=21
Element Seqn Id St Int Rpt
RPPVLRAGVNTVTTLVENKKA RL7A_HUMAN 131 21 -
RPPVLRAGVNTVTTLVENKKA RL7A_MOUSE 131 21 -
RPPVLRAGVNTVTTLVENKKA RL7A_CHICK 131 21 -
RPPVLRAGVNTITSLVENKKA RL7A_FUGRU 131 21 -
KPYAVKYGLNHVVSLIENKKA RL8B_YEAST 127 22 -
KPYAVKYGLNHVVALIENKKA RL8A_YEAST 127 22 -
KPYNVKYGLNHVVALIEAKKA RL8_SCHPO 127 22 -
KPSYVSAGTNTVTKLIEQKKA RL7A_DROME 137 21 -
KPIVVKYGLNHVTYLIEQNKA RL7A_ARATH 123 20 -
KPIVVKYGLNHVTYLIEQSKA RL7A_ORYSA 124 20 -
RANQLRQGINSVVKMVEQKKA RL7A_ANOGA 138 21 -

Motif 6 width=25
Element Seqn Id St Int Rpt
LVHRKTCTTVAFTQVNSEDKGALAK RL7A_HUMAN 192 40 -
LVHRKTCTTVAFTQVNSEDKGALAK RL7A_MOUSE 192 40 -
LVHRKTCTCVAFTQVNPEDKGALAK RL7A_CHICK 192 40 -
LVHRKTCTSVAFTQTNPEDKGALAK RL7A_FUGRU 192 40 -
LVNQKTSAVAALTEVRAEDEAALAK RL8B_YEAST 188 40 -
LVNQKTSAVAALTEVRAEDEAALAK RL8A_YEAST 188 40 -
VIHQKTAAVLAVTEVREEDKNELAS RL8_SCHPO 188 40 -
LVRRKTCTTLALTTVDNNDKANFGK RL7A_DROME 198 40 -
VVHQKTASCLCLTTVKNEDKLEFSK RL7A_ARATH 184 40 -
IVHKKTASVLCLTTVKNEDKLEFSK RL7A_ORYSA 185 40 -
LVYRKTCTCVALTQFENADKPNLAK RL7A_ANOGA 199 40 -

Motif 7 width=21
Element Seqn Id St Int Rpt
NYNDRYDEIRRHWGGNVLGPK RL7A_HUMAN 224 7 -
NYNDRYDEIRRHWGGNVLGPK RL7A_MOUSE 224 7 -
NYNDRYDEIRRHWGGNVLGPK RL7A_CHICK 224 7 -
NYNDRYEEIRRHWGGGILGPK RL7A_FUGRU 224 7 -
NFADKYDEVKKHWGGGILGNK RL8B_YEAST 220 7 -
NFADKYDEVKKHWGGGILGNK RL8A_YEAST 220 7 -
NFSAKYDESRRKWGGGIMGGK RL8_SCHPO 220 7 -
NFNERHEEIRRHWGGGILGSK RL7A_DROME 230 7 -
NFNDKYEEYRKKWGGGIMGSK RL7A_ARATH 216 7 -
NFNDKFDEVRKKWGGGVMGSK RL7A_ORYSA 217 7 -
NFNDRFDDIRRHWGGGLLGPK RL7A_ANOGA 231 7 -