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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGCTACAATTATGGGGCCTCCAGATAGTCCGTATGCCGGAGGCGTGTTTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaagttggttgcgatgtaaggtatcttttgggctgggctttcgttatgttgagctttaattacgtaatcaaatgtatatcgtagggtttcagttgatttctaggttatccatttctcactactcttcttttcagtatgaaatgataagtcggtttattcaggaattctttgttatgtgccccag

Basic information

species Physcomitrella patens
transcript PP1S65_161V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S65_161V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA20G05260.1 (Glycine max), 5'ss of exon 1
GCAGGCTACAATTATGGGGCCTCCAGATAGTCCGTATGCCGGAGGCGTGTTTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaagttggttgcgatgtaaggtatcttttgggctgggctttcgttatgttgagctttaattacgtaatcaaatgt-atatcgtagggtttcagttgatttctaggttatccatttctcactactcttcttttcagtatgaaatgataagtcggtttattcaggaattctttgttatgtgccccag
|| | | ||||||||||| |||||||| ||||| |||||  |||| || || || ||||| ||||||||||| || || ||||| || |||||  | ||||| | |    ||  ||| | |||    ||| || ||   ||    | | ||   || |  | |      || ||    | | | |   ||  ||     |  ||||                                                                                     
GCCGACAACAATTATGGGTCCTCCAGACAGTCCTTATGCTAGAGGTGTTTTCCTAGTCACTATTCATTTCCCTCCAGATTATCCCTTCAAGCCAACCAAGgttttt---atttattgaggtgtc---tat-ttctgtaatgtttctacatttcctttaattctgtaccggttattgtttcttaaaaaataatgtcatgatacatttt------------------------------------------------------------------------------------

upper sequence: PP1S65_161V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ27529 (Selaginella moellendorffii), 5'ss of exon 2
GCAGGCTACAATTATGGGGCCTCCAGATAGTCCGTATGCCGGAGGCGTGTTTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatg--ttaagttggttgcgatgtaaggtatcttttgggctgggctttcgttatgttgagctttaattacgtaatcaaatgtatatcgtagggtttcagttgatttctaggttatccatttctcactactcttcttttcagtatgaaatgataagtcggtttattcaggaattctttgttatgtgccccag
||| || || || ||||| || || ||||| || || || || || ||||| |||||||| |||||||||||||| || ||||| || ||||| || ||||||||  ||    |||  ||||| |   | |  |  |    ||  ||||      |||  |  |    | |||  || | | | | |  | || | ||                                                                                              
GCAAGCGACGATAATGGGTCCGCCCGATAGCCCCTACGCGGGCGGTGTGTTCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAGgtatggctttttctgggagcgatcttttgcagttcctaatttgctcttt------gtttggtctc---ttcgtcttcgattttttctttttggttctccaag------------------------------------------------------------------------------------------
















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|208377427|gb|DC906668.1|DC906668
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAN                         GTTGCCTTCAGGA
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGA
EST: gi|208370792|gb|DC936196.1|DC936196
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAAAAGTAATGGAANC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|162189611|gb|FC365833.1|FC365833
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATA
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATA
EST: gi|100354402|gb|BY945854.1|BY945854
EST:     TCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCCTAGG                         GT-GCCTTCGGGACTAAGGTTTTTCACCCCTA-TATTAATAGTAATGGAA
genomic: TCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCC-TAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCC-TAATATTAATAGTAATGGAA
EST: gi|162267760|gb|FC443750.1|FC443750
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|208355479|gb|DC942599.1|DC942599
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATAAATAGTAATGGAANC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|100352011|gb|BY964660.1|BY964660
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTTAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|162213519|gb|FC389391.1|FC389391
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|162189610|gb|FC365832.1|FC365832
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|100399372|gb|BY954337.1|BY954337
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|100386393|gb|BY951189.1|BY951189
EST:     TCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCCTA-G                         GTTGCCTTCAGGACTAAAGTTTTTCACCCTAATATTAATAGTAATGGAAG
genomic: TCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCC-TAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAG
EST: gi|162247875|gb|FC421765.1|FC421765
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|100394985|gb|BY990020.1|BY990020
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCNTTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAANGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|162209887|gb|FC386029.1|FC386029
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|100447908|gb|CJ972207.1|CJ972207
EST:     TTCTGGNCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGANTAAGGTTTTTCACCCTAATATTAAT
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAAT
EST: gi|208361362|gb|DC935077.1|DC935077
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAAAATAAA-ANTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|100404195|gb|BY955303.1|BY955303
EST:     TTCTGGTCACCATTCATT-CCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAGGGTTTT-CACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|208392544|gb|DC933944.1|DC933944
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGA
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGA
EST: gi|100407393|gb|BY991679.1|BY991679
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|100446504|gb|CJ970803.1|CJ970803
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAN                         GTTGCCTTCAGGACTAANGTTTTTCACCCTAATATNAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|208372127|gb|DC940309.1|DC940309
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAANGNTTTTCACCC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCC
EST: gi|208371528|gb|DC936249.1|DC936249
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|162241124|gb|FC417756.1|FC417756
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGC
EST: gi|208358519|gb|DC930651.1|DC930651
EST:     TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAG                         GTTGCCTTCAGGACTAA
genomic: TTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAA

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: 20

GCAGGCTACAATTATGGGGCCTCCAGATAGTCCGTATGCCGGAGGCGTGTTTCTGGTCACCATTCATTTCCCCCCTGACTATCCATTTAAGCCTCCTAAGgtatgttaag ... tgtgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGCATCTGCCTGGATATTCTCAAGGAGCAATGGAGCCCTGCTTTAACCATAT




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