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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtggaccacatgtgtgaggaagcctgcgttttgtgtgtgagtgtgtgtgttttagcgctggtcaaatgtcacactgagtgggattctttgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCAACTATTCCCATTACCGGAACTGGAATCAACCCAGCAAGAAGCTTTGGCG

Basic information

species Physcomitrella patens
transcript PP1S55_301V6.2
intron # 3
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|100446330|gb|CJ970629.1|CJ970629
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATAGGANTTGCGGTG
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTG
EST: gi|100450101|gb|CJ974094.1|CJ974094
EST:     TCTTCTCTGCNACANACCC-AAGCGCANTGCTCGTGATTCTCATGTGCCG                         GTGTTGNCTCC
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCC
EST: gi|67720457|gb|BJ970716.1|BJ970716
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
EST: gi|208391222|gb|DC933511.1|DC933511
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCT
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCT
EST: gi|162179614|gb|FC355256.1|FC355256
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
EST: gi|208352340|gb|DC906151.1|DC906151
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATAGGATTT
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTT
EST: gi|162181259|gb|FC357041.1|FC357041
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
EST: gi|208377070|gb|DC910844.1|DC910844
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATANGATTTGCGGTGTTCATGGTTCATTTGGCA
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
EST: gi|162181095|gb|FC357267.1|FC357267
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
EST: gi|100442334|gb|BY981358.1|BY981358
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
EST: gi|162246016|gb|FC424388.1|FC424388
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
EST: gi|162158203|gb|FC335246.1|FC335246
EST:     TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCG                         GTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA
genomic: TCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCA

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: 35 (upstream exon), 35 (downstream exon)
Score: 334

CACAGGACTAGCCGCCGAGATCATCGGAACGTTTGTTCTAGTGTACACCGTCTTCTCTGCCACAGACCCCAAGCGCAATGCTCGTGATTCTCATGTGCCGgtaagacttc ... tgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCAACTATTCCCATTACCGGAACTGGAATCAACCCAGCAAGAAGCTTTGGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgttttagcgctggtcaaatgtcacactgagtgggattctttgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCAACTATTCCCATTACCGGAACTGGAATCAACCCAGCAAGAAGCTTTGGCG
                                        ttctttgctcc  CT-rich tract
                                       attcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtggaccacatgtgtgaggaagcctgcgttttgtgtgtgagtgtgtgtgttttagcgctggtcaaatgtcacactgagtgggattctttgctccgcagGTGTTGGCTCCTCTTCCCATAGGATTTGCGGTGTTCATGGTTCATTTGGCAACTATTCCCATTACCGGAACTGGAATCAACCCAGCAAGAAGCTTTGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC