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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATCTAGAACTCCAACGAGGCATATGCGGGCTGAAAACCAGAAACTAACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAGgtaagtcttattttctggtttcttagtttgattggtttggttactaaaatccgttattcttaccaattcatgctcttgtacgctattgtttattcacatagttttatgcgtagtgaattgtagttttgctgttgtctactcatcaatgttgttcactgatgaattactgtctgggttctgcag

Basic information

species Physcomitrella patens
transcript PP1S194_154V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S194_154V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA01G38640.3 (Glycine max), 5'ss of exon 7
GAAAATCTAGAACTCCAACGAGGCATATGCGGGCTGAAAACCAGAAACTAACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAGgtaagtcttattttctggtttcttagtttgattggtttggttactaaaatccgttattcttaccaattcatgctcttgtacgctattgtttattcacatagttttatgcgtagtgaattgtagttttgctgttgtctactcatcaatgttgttcactgatgaattactgtctgggttctgcag
    | |  |    | | | |   | |||    |||||    | |   | |  |||||||||||||| || ||||| |||||  ||||||| |||||||||||   ||| || |    | |   | ||| ||    |    | ||   ||  |  ||||   || ||  ||  |      |  | |  |||||  | ||||                                                                                  
TTGGAGCAGGCTACCGAGCCATAGACATGATAACTGAACCTTATAGGTTGATCCGTCATTGTGAAGTGACAGCCATTCTTGTTTTGTATGGCCTTCCTAGgtat-ccttcttatacaatct---actttcataatctacagtgcttgcatatgacattc---cccatatataatt-----caatttcttttatgtatatag----------------------------------------------------------------------------------
















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|162196430|gb|FC374395.1|FC374395
EST:     ACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAG                         ACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG
genomic: ACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAGgtaagtctta ... ggttctgcagACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG
EST: gi|162251436|gb|FC427701.1|FC427701
EST:     ACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAG                         ACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG
genomic: ACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAGgtaagtctta ... ggttctgcagACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG
EST: gi|162202269|gb|FC378112.1|FC378112
EST:     ACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAG                         ACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG
genomic: ACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAGgtaagtctta ... ggttctgcagACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG
EST: gi|37849179|gb|BJ607187.1|BJ607187
EST:     GTCACTGCCATCCTTGTCCCTGTATGGACTTCCTAG                         ACTACTGACGGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTC
genomic: GTCACTGCCATCCTTGT-CCTGTATGGACTTCCTAGgtaagtctta ... ggttctgcagACTACTGAC-GGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTC
EST: gi|37844792|gb|BJ602800.1|BJ602800
EST:     ACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAG                         ACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG
genomic: ACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAGgtaagtctta ... ggttctgcagACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG
EST: gi|37849460|gb|BJ607468.1|BJ607468
EST:     TGTATGGACTTCCTAG                         ACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG
genomic: TGTATGGACTTCCTAGgtaagtctta ... ggttctgcagACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCG

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: 35 (upstream exon), 31 (downstream exon)
Score: 6

GAAAATCTAGAACTCCAACGAGGCATATGCGGGCTGAAAACCAGAAACTAACTCGTCATTGTGAAGTCACTGCCATCCTTGTCCTGTATGGACTTCCTAGgtaagtctta ... ggttctgcagACTACTGACGGGCTCTATCTTAGCTCACGAACTTATGCATGCCTGGCTTCGTCTGCAAG




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