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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtggcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactgcagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG

Basic information

species Physcomitrella patens
transcript PP1S26_103V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S26_103V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 5
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtggcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactgcagatc-tgagaagttagtg--tagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG---
                                                                                        | |||   ||||    || ||| |   |    |||     |   ||    | |   | | || |  |||     | ||  |  | | ||   ||    | |||| ||  |||||||  |||||||||| ||| ||||||| || ||||| ||||| ||  | ||||||||||| |||||||| ||||| || |      ||||   
---------------------------------------------------------------------------------------gtatggcaatatg---agctctgggagcactcagttcaacatcaacataaaaaaaaatcataattgcgtgatccctaaaatgccttgttgcattgctcctacagCTGCCCTGATGTCCGCTATCTATGAGGAGAACAAGGATGAGGACGGCTTCCTCTACATGACCTACAGCGGGGAGAACACCTTCGGCCTGTTTG---TCTGAGT

upper sequence: PP1S26_103V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G419694_T05 (Zea mays), 3'ss of exon 5
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtggcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactgcagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG
                                               || ||  | | |       |||  ||   || |      ||| ||    |     ||   |     |||  || | || |  | | ||  |    || |        ||   | | | | |||  ||   |     |||||| ||| ||||||| || |||||||| ||| |||||||||| || |||||||| ||  | || ||||| ||||||||||| ||||| ||      |||   
-----------------------------------------------gtctgg-aaagtcaatgcagaaacaac-atgct------cttctgactctgattttgcttcctataagaactgatggtattcggggac-acgatcctcattctcacttgattttacttgcttgcttg---tacccgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGACGAGGATGGGTTCCTCTACATGACTTACAGTGGTGAGAACACCTTCGGACTGCTCTAGATGGC

upper sequence: PP1S26_103V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtg-gcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactg---cagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG
                |  | | || | |||  ||          ||| ||  |  |||||||           ||   ||   ||  |||  | | |  |    ||| |  |  ||  || |      |   ||||    |  |  ||     | | |  | |  |     |     | |  ||  |||||| ||| ||||||| || |||||||| ||| ||||||| || || || ||||| ||  | |||||||| ||||||||||| ||||||||      |||   
---------------gtctg-gaaaataaatacagagacaacatacttctgactctgattttgc----------ttcctataagaa--ttgatggcattcgttgagcatt-tggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctg--tgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC

upper sequence: PP1S26_103V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G014975_T02 (Zea mays), 3'ss of exon 3
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtggcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactgcagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG
                                                                                       |||   |   || | |||        | |        |  |||| ||  |      || | |   | ||  || | |   |         |||  ||||||| ||  |||||||  | ||||| || ||| |||||||||| ||||||||||| ||  | ||||||||||| |||||||| || |||||     |  |   
-------------------------------------------------------------------------------------gtttgccataccat-cgtggggaaaaacaaaataaaacctacctgtccatggtgcccgtgtgta--caatgctgttactttttct-------tgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC

upper sequence: PP1S26_103V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtggcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactgcagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG--
                                                                        |    |     | ||  | | | ||  |||  ||  || | |   || | ||| | ||  |||  |     || |    |    | |  |     |                 |||| ||  | |||||||| |||||||| || |||||||| || ||||| || || ||  | ||||||||||| ||||||||||||||  |  || ||| | |  
-----------------------------------------------------------------------cagcagggccagagccgggcgct-gtg-gcaccgccgtgtgcac-cgtcgctgtctttgctcaccacgtccttgcgcccct--ccttgcaacccactcct------------cacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGG--TGCCGGGGAGCAGCT

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|18344066|gb|BJ176105.1|BJ176105
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGG
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGG
EST: gi|162186577|gb|FC363341.1|FC363341
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|37821375|gb|BJ579441.1|BJ579441
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|67571088|gb|BJ943912.1|BJ943912
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAG
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAG
EST: gi|67571800|gb|BJ944624.1|BJ944624
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|162232018|gb|FC409092.1|FC409092
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|162232017|gb|FC409091.1|FC409091
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|18352101|gb|BJ184155.1|BJ184155
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|208374917|gb|DC956190.1|DC956190
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|162262025|gb|FC437872.1|FC437872
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|37823258|gb|BJ581324.1|BJ581324
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|18327459|gb|BJ159462.1|BJ159462
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|67694401|gb|BJ954634.1|BJ954634
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|37831787|gb|BJ589799.1|BJ589799
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|162276318|gb|FC452620.1|FC452620
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|18331908|gb|BJ163920.1|BJ163920
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACA
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACA
EST: gi|100376476|gb|BY986185.1|BY986185
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|162254652|gb|FC429502.1|FC429502
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|67695168|gb|BJ955401.1|BJ955401
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|18342266|gb|BJ174301.1|BJ174301
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|37821564|gb|BJ579630.1|BJ579630
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|162202071|gb|FC377277.1|FC377277
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|162276592|gb|FC451975.1|FC451975
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
EST: gi|162202124|gb|FC377525.1|FC377525
EST:     TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAG                         CGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC
genomic: TTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCC

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: 16

TTGACGGTTGGACAGTTCGTATATGTGATAAGGAAGCGCATCAAATTGAGTTCCGAAAAGGCCATTTTCATCTTCGTGAAGAATGTGCTACCTCCGACAGgtacgttagt ... gtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtggcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactgcagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT