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PR00029

Identifier
OCTAMER  [View Relations]  [View Alignment]  
Accession
PR00029
No. of Motifs
4
Creation Date
05-APR-1993  (UPDATE 22-JUN-1999)
Title
Octamer-binding transcription factor signature
Database References

INTERPRO; IPR000972
Literature References
1. MULLER, M.M., RUPPERT, S., SCHAFFNER, W. AND MATTHIAS, P.
A cloned octamer transcription factor stimulates transcription from
lymphoid-specific promoters in non-B cells.
NATURE 336 544-551 (1988).
 
2. SCHEIDEREIT, C., CROMLISH, J.A., GERSTER, T., KAWAKAMI, K.,
BALMACEDA, C.-G., CURRIE, R.A. AND RODER, R.G.
A human lymphoid-specific transcription factor that activates
immunoglobulin genes is a homeobox protein.
NATURE 336 551-557 (1988).
 
3. DEKKER, N., COX, M., BOELENS, R., VERRIJZER, C.P., VAN DER VLIET, P.C.
AND KAPTEIN, R.
Solution structure of the POU-specific DNA-binding domain of OCT-1.
NATURE 362 852-855 (1993). 

Documentation
The octamer-binding protein is a transcription factor that binds 
specifically to the octamer motif (ATTTGCAT) of immunoglobulin promoters
and activates these genes. There are two Ig octamer-binding proteins,
designated NF-A1 and NF-A2: NF-A1 is found in all cell types, while
NF-A2 is found only in lymphoid cells. The sequences of these proteins
contain a region that correponds closely to the DNA-binding homeobox
domains and POU transcription factors.
 
OCTAMER is a 4-element fingerprint that provides a signature for both the 
NF-A1 class of nuclear RNA and histone transcription factors, and the 
NF-A2 class of lymphoid-restricted immunoglobulin octamer-binding proteins.
The fingerprint was derived from an initial alignment of 6 sequences: the
motifs were drawn from conserved, glutamine-rich regions, motif 3 
corresponding to the inhibitory domain and motif 4 falling at the start of
the POU domain. Two iterations on OWL22.1 were required to reach
convergence, at which point a true set comprising 23 sequences was
identified. Several partial matches were also found, of which three are
POU sequences that match motifs 3 and 4 (PDM2_DROME, A46196 and DRODPOU28). 
 
An update on SPTR37_9f identified a true set of 15 sequences, and 9
partial matches.
Summary Information
  15 codes involving  4 elements
1 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
415151515
31101
20011
1234
True Positives
O13006        O13007        O57602        OC11_MOUSE    
OCT1_CHICK OCT1_HUMAN OCT1_MOUSE OCT1_XENLA
OCT2_HUMAN OCT2_MOUSE OCT2_PIG Q16648
Q29076 Q91809 SK1A_RAT
True Positive Partials
Codes involving 3 elements
O42276
Codes involving 2 elements
SK1I_RAT
Sequence Titles
O13006      OCT-2 ALPHA TRANSCRIPTION FACTOR - ICTALURUS PUNCTATUS (CHANNEL CATFISH). 
O13007 OCT-2 BETA TRANSCRIPTION FACTOR (OCT2 BETA) - ICTALURUS PUNCTATUS (CHANNEL CATFISH).
O57602 OCT1 TRANSCRIPTION FACTOR - ICTALURUS PUNCTATUS (CHANNEL CATFISH).
OC11_MOUSE OCTAMER-BINDING TRANSCRIPTION FACTOR 11 (OCT-11) - MUS MUSCULUS (MOUSE).
OCT1_CHICK OCTAMER-BINDING TRANSCRIPTION FACTOR 1 (OTF-1) (NF-A1) - GALLUS GALLUS (CHICKEN).
OCT1_HUMAN OCTAMER-BINDING TRANSCRIPTION FACTOR 1 (OTF-1) (NF-A1) - HOMO SAPIENS (HUMAN).
OCT1_MOUSE OCTAMER-BINDING TRANSCRIPTION FACTOR 1 (OTF-1) (NF-A1) - MUS MUSCULUS (MOUSE).
OCT1_XENLA OCTAMER-BINDING TRANSCRIPTION FACTOR 1 (OTF-1) (NF-A1) (XOCT1) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
OCT2_HUMAN OCTAMER-BINDING TRANSCRIPTION FACTOR 2 (OTF-2) (LYMPHOID-RESTRICTED IMMUNOGLOBULIN OCTAMER BINDING PROTEIN NF-A2) (OCT-2 FACTOR) - HOMO SAPIENS (HUMAN).
OCT2_MOUSE OCTAMER-BINDING TRANSCRIPTION FACTOR 2 (OTF-2) (LYMPHOID-RESTRICTED IMMUNOGLOBULIN OCTAMER BINDING PROTEIN NF-A2) (OCT-2 FACTOR) - MUS MUSCULUS (MOUSE).
OCT2_PIG OCTAMER-BINDING TRANSCRIPTION FACTOR 2 (OTF-2) (LYMPHOID-RESTRICTED IMMUNOGLOBULIN OCTAMER BINDING PROTEIN NF-A2) (OCT-2 FACTOR) - SUS SCROFA (PIG).
Q16648 OCT-2 PROTEIN - HOMO SAPIENS (HUMAN).
Q29076 OCTAMER BINDING PROTEIN 1 - SUS SCROFA (PIG).
Q91809 MATERNAL TRANSCRIPTION FACTOR - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
SK1A_RAT TRANSCRIPTION FACTOR SKN-1A - RATTUS NORVEGICUS (RAT).

O42276 OCTAMER-BINDING TRANSCRIPTION FACTOR 1 - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).

SK1I_RAT TRANSCRIPTION FACTOR SKN-1I - RATTUS NORVEGICUS (RAT).
Scan History
OWL22_1    2  100  NSINGLE    
OWL26_0 1 250 NSINGLE
SPTR37_9f 3 75 NSINGLE
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
GDIQQLLQLQQLVLVP OCT2_HUMAN 100 100 -
QLQQQNLNLQQFVLVH OCT1_HUMAN 181 181 -
QLQQQNLNLQQFVLVH OCT1_CHICK 175 175 -
KDIQQLLQLQQLVLVP RATASOBB 62 62 -
GDIQQLLQLQQLVLVP RATOBTF 101 101 -
GDMASLHPLQQLVLVP OC11_MOUSE 79 79 -

Motif 2 width=16
Element Seqn Id St Int Rpt
QFIISQTPQGQQGLLQ OCT1_CHICK 199 8 -
QFLLPQAQQSQPGLLP RATOBTF 125 8 -
QFLLPQAQQSQPGLLP RATASOBB 86 8 -
QFIISQTPQGQQGLLQ OCT1_HUMAN 205 8 -
QFLLPQAQQSQPGLLP OCT2_HUMAN 124 8 -
QFLLSQTPPGQQGLQP OC11_MOUSE 102 7 -

Motif 3 width=13
Element Seqn Id St Int Rpt
PQQTQGALLTSQP RATASOBB 109 7 -
PQQSQANLLQSQP OCT1_CHICK 223 8 -
PQQSQANLLQSQP OCT1_HUMAN 229 8 -
PQQTQGALLTSQP OCT2_HUMAN 147 7 -
PQQQSTLLLPQTG OC11_MOUSE 123 5 -
PQQTQGALLTSQP RATOBTF 148 7 -

Motif 4 width=12
Element Seqn Id St Int Rpt
EEPSDLEELEQF RATASOBB 172 50 -
EEPSDLEELEQF OCT1_HUMAN 280 38 -
EEPSDLEELEQF OCT2_HUMAN 194 34 -
DEPTDLEELEKF OC11_MOUSE 176 40 -
EEPSDLEELEQF RATOBTF 179 18 -
EEPSDLEELEQF OCT1_CHICK 274 38 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
QLQQQNLNLQQFVLVH OCT1_CHICK 175 175 -
QLQQQNLNLQQFVLVH OCT1_HUMAN 181 181 -
QLQQQNLNLQQYVLVH OCT1_XENLA 195 195 -
QLQQQNLNLQQYVLVH Q91809 195 195 -
QLQQQNLNLQQFVLVH OCT1_MOUSE 182 182 -
QLQQQNLNLQQFVLGH Q29076 181 181 -
GDIQQLLQLQQLVLVP OCT2_HUMAN 100 100 -
GDIQQLLQLQQLVLVP OCT2_MOUSE 100 100 -
GDIQQLLQLQQLVLVP Q16648 101 101 -
GDIQQLLQLQQLVLVP O13007 110 110 -
GDIQQLLQLQQLVLVP O13006 110 110 -
GDIQQILQLQQLVLVP OCT2_PIG 101 101 -
GDMASLHPLQQLVLVP SK1A_RAT 79 79 -
GDMASLHPLQQLVLVP OC11_MOUSE 79 79 -
QLQPTGLNLQQFVLVQ O57602 106 106 -

Motif 2 width=16
Element Seqn Id St Int Rpt
QFIISQTPQGQQGLLQ OCT1_CHICK 199 8 -
QFIISQTPQGQQGLLQ OCT1_HUMAN 205 8 -
QFIISQTPQGQQGLLQ OCT1_XENLA 219 8 -
QFIISQTPQGQQGLLQ Q91809 219 8 -
QFIISQTPQGQQGLLQ OCT1_MOUSE 206 8 -
QFIISQTPQGQQGLLQ Q29076 205 8 -
QFLLPQAQQSQPGLLP OCT2_HUMAN 124 8 -
QFLLPQAQQSQPGLLP OCT2_MOUSE 124 8 -
QFLLPQAQQSQPGLLP Q16648 125 8 -
QFLLPQAQQGQQGLLQ O13007 134 8 -
QFLLPQAQQGQQGLLQ O13006 134 8 -
QFLLPQAQQSQPGLLP OCT2_PIG 125 8 -
QFLLSQTPPGQQGLQP SK1A_RAT 102 7 -
QFLLSQTPPGQQGLQP OC11_MOUSE 102 7 -
QFIISPSPQGQTGLLQ O57602 129 7 -

Motif 3 width=13
Element Seqn Id St Int Rpt
PQQSQANLLQSQP OCT1_CHICK 223 8 -
PQQSQANLLQSQP OCT1_HUMAN 229 8 -
PQQSQANLLQSQP OCT1_XENLA 243 8 -
PQQSQANLLQSQP Q91809 243 8 -
PQQSQANLLQPQP OCT1_MOUSE 230 8 -
PQQSQANLLQSQP Q29076 229 8 -
PQQTQGALLTSQP OCT2_HUMAN 147 7 -
PQQTQGALLTSQP OCT2_MOUSE 147 7 -
PQQTQGALLTSQP Q16648 148 7 -
PQQNQGGLLSAPP O13007 157 7 -
PQQNQGGLLSAPP O13006 157 7 -
PQQTQGALLTSQP OCT2_PIG 148 7 -
PQQQSTLLLPQTG SK1A_RAT 123 5 -
PQQQSTLLLPQTG OC11_MOUSE 123 5 -
LPQSQAHILQPQS O57602 155 10 -

Motif 4 width=12
Element Seqn Id St Int Rpt
EEPSDLEELEQF OCT1_CHICK 274 38 -
EEPSDLEELEQF OCT1_HUMAN 280 38 -
EEPSDLEELEQF OCT1_XENLA 294 38 -
EEPSDLEELEQF Q91809 294 38 -
EEPSDLEELEQF OCT1_MOUSE 281 38 -
EEPSDLEELEQF Q29076 280 38 -
EEPSDLEELEQF OCT2_HUMAN 194 34 -
EEPSDLEELEQF OCT2_MOUSE 178 18 -
EEPSDLEELEQF Q16648 195 34 -
EEPSDLEELEQF O13007 197 27 -
EEPSDLEELEQF O13006 197 27 -
EEASDLEELEQF OCT2_PIG 195 34 -
DEPTDLEELEKF SK1A_RAT 176 40 -
DEPTDLEELEKF OC11_MOUSE 176 40 -
EEASELEELEQF O57602 202 34 -