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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATAGGCATTCGAATGCGTTAGTGGATGTGCTGCCGCCTGAAGCAGATTCTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttcatttatttctatgacctttatattgatatttttgtcgatgtggagaggtgtatgtggaacgagcagtgtagccctcttgcatgttatctca...

Basic information

species Physcomitrella patens
transcript PP1S79_171V6.1
intron # 1
splice site 5'
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|100364097|gb|BY966713.1|BY966713
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100438790|gb|BY961804.1|BY961804
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100446543|gb|CJ970842.1|CJ970842
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100382544|gb|BY969129.1|BY969129
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGGAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|208357606|gb|DC914020.1|DC914020
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCANAAACNAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100361678|gb|BY947767.1|BY947767
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAAACA-GAGATTAGGGAAGCTGTGGA
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAA-CAAGAGATTAGGGAAGCTGTGGA
EST: gi|208380173|gb|DC927452.1|DC927452
EST:     ACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: ACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100430108|gb|BY978251.1|BY978251
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100395308|gb|BY953672.1|BY953672
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAAACA-GAGATTAGGGA-GCTGTGGA
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAA-CAAGAGATTAGGGAAGCTGTGGA
EST: gi|100444325|gb|BY982354.1|BY982354
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100439369|gb|BY980229.1|BY980229
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAAACA-GAGATTAGGGA-GCTGTGGA
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAA-CAAGAGATTAGGGAAGCTGTGGA
EST: gi|208351738|gb|DC913695.1|DC913695
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100389731|gb|BY952537.1|BY952537
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100390407|gb|BY952815.1|BY952815
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGGAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100372217|gb|BY985491.1|BY985491
EST:     TAGCATCTCTCTGTTGACACAATCCGGAGAGGCG-GATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGGAGCTGTGGAG
genomic: TAGCATCTCTCTGTTGACACAATCCG-AGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100359161|gb|BY965621.1|BY965621
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|18360609|gb|BJ192672.1|BJ192672
EST:     CCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100375287|gb|BY948824.1|BY948824
EST:     TAGCATCTCTCTGTTGACANCA-TCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAGGAGATTAGGGAAGCTGTGGAG
genomic: TAGCATCTCTCTGTTGACA-CAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|208365017|gb|DC943354.1|DC943354
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100384869|gb|BY969604.1|BY969604
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATANNNNNNNNNTGATATTCAGAAACAAGAGATTAGGGGAGCTGTGGA
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTG-TGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGA
EST: gi|162254099|gb|FC429623.1|FC429623
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|208351728|gb|DC909780.1|DC909780
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|18369533|gb|BJ201620.1|BJ201620
EST:     CCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100425214|gb|BY977030.1|BY977030
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|208352375|gb|DC906172.1|DC906172
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100402429|gb|BY954832.1|BY954832
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGGAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100360225|gb|BY966078.1|BY966078
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
EST: gi|100425805|gb|BY977129.1|BY977129
EST:     CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCCGATGTGTCCTATAAT                         GATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG
genomic: CTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 29 (downstream exon)
Score: 21

TCATAGGCATTCGAATGCGTTAGTGGATGTGCTGCCGCCTGAAGCAGATTCTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttca ... ttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAGCTTCCACTTACTCATCACGAGTTATACAAGCAGATTGGTATTGACCCAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATAGGCATTCGAATGCGTTAGTGGATGTGCTGCCGCCTGAAGCAGATTCTAGCATCTCTCTGTTGACACAATCCGAGAAGCCTGATGTGTCCTATAATgtacgtttcatttatttctatgacctttatattgatatttttgtcgatgtggagaggtgtatgtggaacgagcagtgtagccctcttgcatgttatctca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC