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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagggtttaaaagcggcagcattctttgtgactgaagtgatttctcgcaatctgcgtaaaccactggcatttctgttgggcgtctgtggcgctaagtcttatccgctgtttgcttaatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTTATACTTCAACAGCAACAGCAGCACCTTCACCAACAACCGCAGCAACATC

Basic information

species Physcomitrella patens
transcript PP1S69_37V6.1
intron # 6
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|162158034|gb|FC334448.1|FC334448
EST:     ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAG                         GCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
genomic: ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAGgttagggttt ... taatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
EST: gi|162198001|gb|FC374003.1|FC374003
EST:     ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAG                         GCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
genomic: ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAGgttagggttt ... taatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
EST: gi|162158048|gb|FC334449.1|FC334449
EST:     ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAG                         GCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
genomic: ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAGgttagggttt ... taatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
EST: gi|162270101|gb|FC446801.1|FC446801
EST:     ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAG                         GCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
genomic: ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAGgttagggttt ... taatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
EST: gi|162198000|gb|FC374002.1|FC374002
EST:     ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAG                         GCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
genomic: ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAGgttagggttt ... taatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
EST: gi|162188452|gb|FC365050.1|FC365050
EST:     ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAG                         GCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
genomic: ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAGgttagggttt ... taatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
EST: gi|162188453|gb|FC365051.1|FC365051
EST:     ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAG                         GCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT
genomic: ATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAGgttagggttt ... taatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTT

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: 27 (upstream exon), 35 (downstream exon)
Score: 22

TTCCATGATTGATCCACATGACCTCCGCTATCAACAACCCGGTGATATGGATTTCAATACTTACACAGCTCATCAGCATCAGTCAATGCCAATGACTCAGgttagggttt ... taatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTTATACTTCAACAGCAACAGCAGCACCTTCACCAACAACCGCAGCAACATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgttgggcgtctgtggcgctaagtcttatccgctgtttgcttaatgtgcagGCGTTAAATACAGATAAATATAACGCTTATATGTTGCAACAGCACCAGTTTATACTTCAACAGCAACAGCAGCACCTTCACCAACAACCGCAGCAACATC
                                          gcttaat  putative branch site (score: 22)
                                       tttgctt  CT-rich tract
                                            ttaatgt  TA-rich tract