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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttagcaaagagagattgctttgagctggcttttttctttctcataatgggtaaaatctctggcttgtctctgatctttcgacgttctgtgcaatcagGTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCTTCTTAATGAATCTGAGTTGCACAATCGCCAACTCAAG

Basic information

species Physcomitrella patens
transcript PP1S422_18V6.1
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|208368699|gb|DC940036.1|DC940036
EST:     ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGG                         GTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCANTACAAAATGCGATTCT
genomic: ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGGgtaatttctt ... gtgcaatcagGTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT
EST: gi|208366662|gb|DC931319.1|DC931319
EST:     ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGG                         GTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAA-TGCGATTCT
genomic: ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGGgtaatttctt ... gtgcaatcagGTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT
EST: gi|208389601|gb|DC945825.1|DC945825
EST:     ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGG                         GTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT
genomic: ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGGgtaatttctt ... gtgcaatcagGTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT
EST: gi|100400310|gb|BY954413.1|BY954413
EST:     CAGTGAACCGTGTCACTATNTTGACAGACAAATTTGGGCAGCCTNNAAGG                         GTT-GCATATGTGGAGTTTTNNNGGAG-TCGAG-CAGTACAAAATGCGAT
genomic: CAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTA-AAGGgtaatttctt ... gtgcaatcagGTTTGCATATGTGGAGTTTTT--GGAGGTCGAGGCAGTACAAAATGCGAT
EST: gi|208376819|gb|DC906802.1|DC906802
EST:     ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGG                         GTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT
genomic: ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGGgtaatttctt ... gtgcaatcagGTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT
EST: gi|162266936|gb|FC441789.1|FC441789
EST:     ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGG                         GTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT
genomic: ACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGGgtaatttctt ... gtgcaatcagGTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT
EST: gi|67697499|gb|BJ957732.1|BJ957732
EST:     ATTTTGACAGACAAANTTGGGNCAGCCTAAAGG                         GTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT
genomic: ATTTTGACAGACAAATTTGGG-CAGCCTAAAGGgtaatttctt ... gtgcaatcagGTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCT

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: 32 (upstream exon), 30 (downstream exon)
Score: 7

ATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGTGGGACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTAAAGGgtaatttctt ... gtgcaatcagGTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCTTCTTAATGAATCTGAGTTGCACAATCGCCAACTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgggtaaaatctctggcttgtctctgatctttcgacgttctgtgcaatcagGTTTGCATATGTGGAGTTTTTGGAGGTCGAGGCAGTACAAAATGCGATTCTTCTTAATGAATCTGAGTTGCACAATCGCCAACTCAAG
                         ctctgat  putative branch site (score: 7)
        taaaatct  TA-rich tract