Skip to another splice site:
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 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacgttgtcttcaaccttacttgccgtaagcggcagagccggtgcaccacaacaatgaggctctagatgcttaactcccaaatcactaatttttgtgacgataatgttgctgaatagtgtcggtgaatggtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCAG

Basic information

species Physcomitrella patens
transcript PP1S100_119V6.1
intron # 1
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|208354589|gb|DC918671.1|DC918671
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162201084|gb|FC378215.1|FC378215
EST:     GAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGC
genomic: GAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTAC-TTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGC
EST: gi|162256714|gb|FC433232.1|FC433232
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|208383018|gb|DC927768.1|DC927768
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|18335963|gb|BJ167984.1|BJ167984
EST:     CGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162243687|gb|FC421834.1|FC421834
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|18364720|gb|BJ196793.1|BJ196793
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162234198|gb|FC410776.1|FC410776
EST:     CCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162216233|gb|FC392650.1|FC392650
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162149644|gb|FC325837.1|FC325837
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162234199|gb|FC410777.1|FC410777
EST:     CCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162261340|gb|FC437773.1|FC437773
EST:     AGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: AGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162212533|gb|FC388509.1|FC388509
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162199824|gb|FC376404.1|FC376404
EST:     AGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: AGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|208398013|gb|DC924899.1|DC924899
EST:     CCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGNCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|208382553|gb|DC923195.1|DC923195
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|19788947|gb|BQ041013.1|BQ041013
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162246286|gb|FC419900.1|FC419900
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|67695108|gb|BJ955341.1|BJ955341
EST:     CGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162249971|gb|FC427072.1|FC427072
EST:     GAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: GAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|208399226|gb|DC916581.1|DC916581
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162202011|gb|FC377217.1|FC377217
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|67701042|gb|BJ961275.1|BJ961275
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|208386827|gb|DC953494.1|DC953494
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162203252|gb|FC379349.1|FC379349
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162249972|gb|FC427073.1|FC427073
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162203253|gb|FC379350.1|FC379350
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|208390867|gb|DC945898.1|DC945898
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162170155|gb|FC347067.1|FC347067
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|162225082|gb|FC401706.1|FC401706
EST:     TGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: TGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
EST: gi|208382474|gb|DC928008.1|DC928008
EST:     CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAG                         GTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA
genomic: CTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCA

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: 25 (upstream exon), 31 (downstream exon)
Score: 5

GTTCAAGGCTCAAAACGCGCCGACTGAGAATGCAGCGCCAGCAACTTCGCCTGGTGGCCGAGCCGTCCCAACTAACGAGGAGTTAATGGAAAGCAGCCAGgtaaacgttg ... gtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaatttttgtgacgataatgttgctgaatagtgtcggtgaatggtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCAG
 cactaat  putative branch site (score: 5)
                ataatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacgttgtcttcaaccttacttgccgtaagcggcagagccggtgcaccacaacaatgaggctctagatgcttaactcccaaatcactaatttttgtgacgataatgttgctgaatagtgtcggtgaatggtcactgcagGTACTTCTCGGTGCTGCCCAGGGCCAAAAAATTGAGAACACCAAGCTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT