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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGGACTTATAGGAGCGGGAACCAATAACGCCCGAATTGCTGGAATGCTTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttctttaccttaattcattatgcatctaattattctgttactttgcgttattctttgtttagggctggatgacaacatgttgatgacatgcag

Basic information

species Physcomitrella patens
transcript PP1S3_553V6.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S3_553V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GLYMA12G13410.1 (Glycine max), 5'ss of exon 21
TTTGGGACTTATAGGAGCGGGAACCAATAACGCCCGAATTGCTGGAATGCTTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttctttaccttaattcattatgcatctaattattctgttactttgcgttattctttgtttagggctggatgacaacatgttgatgacatgcag
 ||||| || ||||| || ||||| || || || ||||||||||| |||||||||||||| ||||| || || ||||||||  | ||||| || || |||||| ||||  |   || |  ||    | |  ||  ||||| |  || ||| |  | ||     |||| ||           | | |   | |  |  ||
CTTGGGTCTGATAGGTGCTGGAACGAACAATGCTCGAATTGCTGGCATGCTTCGCAATCTTTCTAGTTATTACTACAAGGATACCAGCCTTCTATTCTGTgtaagctttct---ctaagctc----tcctcctccttatttt-ctaatttccactgtt-----tttatggtcacccattttcttttaccttatctatag
















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|162280078|gb|FC456472.1|FC456472
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|37835828|gb|BJ593840.1|BJ593840
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGGCCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|37848700|gb|BJ606708.1|BJ606708
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCNTACTCTTTTGT                         GTTAGGATTGCACAAGGCNTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|162176023|gb|FC351024.1|FC351024
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|18336901|gb|BJ168924.1|BJ168924
EST:     CTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: CTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|162176009|gb|FC351023.1|FC351023
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|37830143|gb|BJ588155.1|BJ588155
EST:     ATTACAAGGACCCAAGGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: ATTACAAGGACCCAA-GCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|37846451|gb|BJ604459.1|BJ604459
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|67578805|gb|BJ950972.1|BJ950972
EST:     CTCTCTAGCTACTATTACAAGGACCCAAGCNTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: CTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|37827765|gb|BJ585777.1|BJ585777
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|162163326|gb|FC339652.1|FC339652
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|37839139|gb|BJ597147.1|BJ597147
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCNTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|37824468|gb|BJ582534.1|BJ582534
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|37826418|gb|BJ584430.1|BJ584430
EST:     TTCGCAATCTCTNTAGCTANTATTACAAGGGCCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|67507537|gb|BJ940419.1|BJ940419
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
EST: gi|162186176|gb|FC362108.1|FC362108
EST:     TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGT                         GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC
genomic: TTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTC

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: 9 (upstream exon), 27 (downstream exon)
Score: 1

TTTGGGACTTATAGGAGCGGGAACCAATAACGCCCGAATTGCTGGAATGCTTCGCAATCTCTCTAGCTACTATTACAAGGACCCAAGCCTACTCTTTTGTgtatgcttct ... tgacatgcagGTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA




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