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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGTGGAGGAGTACGCACAGAAGTACCCTGAGGAGGGTGCCGAGTTCAAGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaatcagacttcttggtggtgcgagatttcaacagttgtggtctgttaaagtctgtcatttgcgataatgggtaggtttgcgattacgtgtctgtgtaatgtgagtggaagtggaattgtaattggtgtcggaataggctgtcgatggtattttatcgagggagtgatggaatttgtgggtatgatgcag

Basic information

species Physcomitrella patens
transcript PP1S120_127V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S120_127V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 5'ss of exon 6
TGCTGTGGAGGAGTACGCACAGAAGTACCCTGAGGAGGGTGCCGAGTTCAAGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaatcagacttcttggtggt--gcgagatttcaacagttgtggtc-tgttaaagtctgtcatttgcgataatgggtaggtttgcgattacgtgtctgtgtaatgtgagtggaagtggaattgtaattggtgtcggaataggctgtcgatggtattttatcgagggagtgatggaatttgtgggtatgatgcag
     | |  |  || |   |||| || || ||||| | ||| ||||| ||     | |||   ||||||||||||| ||| ||||| ||||| ||||||||||||| |    ||||  ||||  |     |  ||| | ||||  |  || | |  ||| || | ||||  |  ||     |  ||| |  |||                                                                                                        
CAAATTTGCAGCTTATGAGAAGAAATATCCGGAGGAAGCTGCAGAGTTGAAATCTATTATCTCAGGTGAATTGCCCGTTGGTTGGGAGAAGGCACTTCCTgtaagtaga----actttctggtaatctataacgttttatcagtattcttcatatataaggctcttattttaggcaactta-aaattttcatttag-------------------------------------------------------------------------------------------------------
















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|162193500|gb|FC370403.1|FC370403
EST:     AGCGGTGAATTGCCCGATGGCTGGGACAACGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|162230960|gb|FC407215.1|FC407215
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|162219706|gb|FC395910.1|FC395910
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|162176306|gb|FC352763.1|FC352763
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|162166851|gb|FC343028.1|FC343028
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|162241577|gb|FC415505.1|FC415505
EST:     GGCTGGGACAAGGCTCTTCCT                         TCTTTCACCCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGA
genomic: GGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|162198697|gb|FC374817.1|FC374817
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|162155567|gb|FC331011.1|FC331011
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|162219889|gb|FC396704.1|FC396704
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|100356519|gb|BY946406.1|BY946406
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|100400286|gb|BY954401.1|BY954401
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
EST: gi|162209022|gb|FC385574.1|FC385574
EST:     AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCT                         TCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG
genomic: AGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGG

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), 35 (downstream exon)
Score: 61

TGCTGTGGAGGAGTACGCACAGAAGTACCCTGAGGAGGGTGCCGAGTTCAAGCAGTTGATCAGCGGTGAATTGCCCGATGGCTGGGACAAGGCTCTTCCTgtaagtaaat ... tatgatgcagTCGTTCACTCCCGAGGACGCTGGTGACGCCACCCGCAACTTGTCCCAGAGGTGTTTGAACGCCTTGGCTAGGACTCTTCCAGGACTTATCGGTGGCAGTG




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