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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcacaagatccaaacgtcattgaggacgctgtgtatcagtggatgaatgatagcaagcctttcttcacagaaacaggctttcatttacccccagagttgtgtggacatttgctgttagttattgtgtattaagtacgagtgctgacattgagcacttgcttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAGCTCACACCCTCTTTGGCTCGCCTTGTTCTGCAGAAAGG

Basic information

species Physcomitrella patens
transcript PP1S407_7V6.3
intron # 4
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67717425|gb|BJ967684.1|BJ967684
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|100388601|gb|BY970749.1|BY970749
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|162161524|gb|FC338731.1|FC338731
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|18368288|gb|BJ200373.1|BJ200373
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|18364681|gb|BJ196754.1|BJ196754
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAA
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAA
EST: gi|18369465|gb|BJ201552.1|BJ201552
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAA
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAA
EST: gi|162184196|gb|FC360463.1|FC360463
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|18325312|gb|BJ157308.1|BJ157308
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGC
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGC
EST: gi|67574848|gb|BJ947672.1|BJ947672
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|18345047|gb|BJ177088.1|BJ177088
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGA
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGA
EST: gi|208354688|gb|DC934180.1|DC934180
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|208346695|gb|DC913341.1|DC913341
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|67577876|gb|BJ950043.1|BJ950043
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|100362562|gb|BY947415.1|BY947415
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
EST: gi|67712636|gb|BJ966085.1|BJ966085
EST:     AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAG                         CTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG
genomic: AATCGGAGGACCTTTACACCCGTAAAGCTGGCGAAGAGATCGTTGGACAGgttcacaaga ... cttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagttattgtgtattaagtacgagtgctgacattgagcacttgcttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAGCTCACACCCTCTTTGGCTCGCCTTGTTCTGCAGAAAGG
                                         cttgctt  CT-rich tract
     ttattgtgtattaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcacaagatccaaacgtcattgaggacgctgtgtatcagtggatgaatgatagcaagcctttcttcacagaaacaggctttcatttacccccagagttgtgtggacatttgctgttagttattgtgtattaagtacgagtgctgacattgagcacttgcttgatgcagCTCTATAATTTTGAGGACAAAGGTGGTAGAAAGGTTGCCCTTCGACCCGAGCTCACACCCTCTTTGGCTCGCCTTGTTCTGCAGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG