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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttccctgagatttgagctacttttcacttttgcgaatctttttaaaaaatgtggtgtaacattttcattcgttttctgttcag

Basic information

species Physcomitrella patens
transcript PP1S63_54V6.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GRMZM2G107082_T01 (Zea mays), 5'ss of exon 9
TGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaa--------gcttccctgag-------atttgagct----acttttcacttttgcgaatctttttaaaaaatgtggtgtaacattttcattcgttttctgttcag
||||||||||||||||||  |  |  | || || ||||| ||||||||||||||||||||  | || ||||| |||||||| |||||| |  | || ||||||          ||  | | ||       | | | |||    ||   |||  | ||   | ||  || |    |    |||   ||   ||  |  ||    |||||
TGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGTGGCATAGCTAACTTCACTGATGTTGCTACCACATTCAATGGCATCATCCGAGCCTTAAGGGAGAAGgtacctaagaccactcactttagaatcctcactggtgcttggcaccactcatatctgttcacctaattgattcttcacctgttttatcgccacacaattcactttcag

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA03G38810.1 (Glycine max), 5'ss of exon 10
TGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttccctgagatttgagctacttttcacttttgcgaatctttttaaaaaat-gtggtgtaacattttcattcgttttctgttcag
 |||||||| ||||||||  |  || | || || ||||| || ||||||||||||||||| || || |||||||| || ||||||||| ||   || |||||  | |  | | || | |   ||   | |  |||   |   |   ||| |||  |  ||   |    |  ||||   | | | |     
CGATGGCCGTAAGAGAGCCCTTCTTATTGGAGGTGGCATAGCAAACTTCACTGATGTTGCTGCCACATTCAACGGGATTATTCGAGCCCTGAAAGAGAAGgtgtgttatcgttagttgtattctgaatct-gcttcaacttgttaatttgaaagtttatgagttggtttcctcatcactctacag-----

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: AT1G09430.1 (Arabidopsis thaliana), 5'ss of exon 10
TGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttccctg-agatttgagctacttttc--acttttgcgaatct-ttttaaaaaatgtg-gtgtaacattttcattcgttttctgttcag-------------------------
||| || || ||  ||||| |  |  | || ||||||||||| || ||||||||||| ||||| ||||||||||| |||||||||||  |  | ||||||||   ||| |    | | || ||  |     |  ||  |||| | | | |||| |  ||  || | | ||   |       |   ||  | | |                         
TGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttctcacaaactttagtgaacgaacaaacagttgctactgtattttgatgaagatgagaggaatgctcaagaatgaaatcgatgctgacctttttttgtgtgccatgagcag

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 5'ss of exon 10
TGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttccctgagatt----tgagctacttttcacttttgcgaatct--ttttaaa---aaatgtggtgtaacattttcattcgttttctgttcag----------
||||||||| ||||||||  |  |  | || || || ||||||||||||||||||||||| || |||||||| || ||  | || ||  ||   || |||||  | |    |   |||    |       | ||   | || | | |||  |  ||||   || | || |  ||| ||||  ||  |||| |  |             
TGATGGCCGTAAGAGAGCCCTTCTCATTGGAGGGGGTATTGCTAACTTCACTGATGTTGCTGCCACTTTCAATGGGATTGTCCGGGCTCTGAAGGAGAAGgtgtgatcaagttgaattattctctctggatcttggttgtttcaattctcatcctaaattcaagtttgcttcaacttttttttttctttttttctttttttctgacag

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|208365149|gb|DC946778.1|DC946778
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|18339126|gb|BJ171152.1|BJ171152
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|162235867|gb|FC412418.1|FC412418
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|18336575|gb|BJ168597.1|BJ168597
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|208364467|gb|DC958036.1|DC958036
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|37846736|gb|BJ604744.1|BJ604744
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|22492495|gb|BU052418.1|BU052418
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|37849163|gb|BJ607171.1|BJ607171
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|37841322|gb|BJ599330.1|BJ599330
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|7648273|gb|AW739256.1|AW739256
EST:     GCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: GCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|67697641|gb|BJ957874.1|BJ957874
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|22132424|gb|BQ827155.1|BQ827155
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|208385420|gb|DC956632.1|DC956632
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|37845681|gb|BJ603689.1|BJ603689
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|162162206|gb|FC337988.1|FC337988
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC

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: 33 (upstream exon), 28 (downstream exon)
Score: 14

TGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGCCCCAACTACTTGAAGGGTCTGGCAAACATGCGGGCTCTAAGTGAAGAGA




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