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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttacgctctcatcccttttcgaaatgttttctttagatatatttctagctgcccatccgttgaagacaaagtctagcgagtcttttatatgacggaatttctatattctggtgaaaatggcaatcagctgaaaattccaccttttaataccattttaatatgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCGGAGCCTACAGTCATCACTTAAATATTATGCTAATGGCAAGCAGAGGAAA

Basic information

species Physcomitrella patens
transcript PP1S4_12V6.2
intron # 18
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|37829340|gb|BJ587352.1|BJ587352
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162276462|gb|FC452465.1|FC452465
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|18341150|gb|BJ173183.1|BJ173183
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|18338573|gb|BJ170597.1|BJ170597
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162184967|gb|FC362413.1|FC362413
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162187300|gb|FC363458.1|FC363458
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162184968|gb|FC362414.1|FC362414
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|208382001|gb|DC923846.1|DC923846
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162206764|gb|FC383237.1|FC383237
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|67725611|gb|BJ975870.1|BJ975870
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162206765|gb|FC383238.1|FC383238
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|37850179|gb|BJ608187.1|BJ608187
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGCAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162257952|gb|FC433838.1|FC433838
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162175774|gb|FC352076.1|FC352076
EST:     CTGATCCTGCCAAGATATTTGAACCCTCTGCCGAGGCGTTGGCACCTTTT                         GTGGAGGTAGCTTTAAAGCTTTTGAAAATGGAGGAGTTCACAGGCCGCTTG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162178505|gb|FC354957.1|FC354957
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162178864|gb|FC354796.1|FC354796
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|67692041|gb|BJ952274.1|BJ952274
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|37828076|gb|BJ586088.1|BJ586088
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162159186|gb|FC334357.1|FC334357
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162196533|gb|FC374420.1|FC374420
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162185023|gb|FC362469.1|FC362469
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|67693718|gb|BJ953951.1|BJ953951
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162263231|gb|FC439052.1|FC439052
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|67727198|gb|BJ977457.1|BJ977457
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|67695071|gb|BJ955304.1|BJ955304
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162231044|gb|FC406155.1|FC406155
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162180376|gb|FC355797.1|FC355797
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162263230|gb|FC439051.1|FC439051
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG

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), 35 (downstream exon)
Score: 22

AACTGGTTCAGTGGGCGCTACGATTCGTCTGTACATTGAGCAATACGAAGCTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCGGAGCCTACAGTCATCACTTAAATATTATGCTAATGGCAAGCAGAGGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatggcaatcagctgaaaattccaccttttaataccattttaatatgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCGGAGCCTACAGTCATCACTTAAATATTATGCTAATGGCAAGCAGAGGAAA
                                      ttttaat  putative branch site (score: 22)
                           ttttaataccatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttacgctctcatcccttttcgaaatgttttctttagatatatttctagctgcccatccgttgaagacaaagtctagcgagtcttttatatgacggaatttctatattctggtgaaaatggcaatcagctgaaaattccaccttttaataccattttaatatgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCGGAGCCTACAGTCATCACTTAAATATTATGCTAATGGCAAGCAGAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA