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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttgttggcctttccatcattgtctagtacatgttatagatctcaacctcagcctgctactatcacttgattaatcttgtttgtcttttcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG

Basic information

species Physcomitrella patens
transcript PP1S51_241V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S51_241V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT3G53580.1 (Arabidopsis thaliana), 3'ss of exon 7
atcttgttggcctttccatcattgtctagtacatgttatagatc-tcaacctcagcctgc-tactatcacttgattaat-cttgtttgtcttttcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG
   |        |  ||   ||  || | || |  |   || |  | |    ||| ||   ||   | |  || ||||| |||     |  ||  |    |||| || |||  ||||||||||||||||||||||||  | |||||||| |||||    |||||||| ||||| |||
--gtccgcaaattccccccaatcttcgaatataattctcagttgattataaacagtctctgtatccttatatgcttaatgcttacgcatacttaaaactgcagGAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG

upper sequence: PP1S51_241V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------atcttgttggcctttccatcattgtctagtacatgttatagatctcaacctcagcctgctactatcacttgatt---aatcttgtt--tgtcttttcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG
                                      || |   | |||| |  |  |||||  |||   ||| ||||     |   |  ||||| |    |   ||  ||   || |||  |  | || ||    |  |||| || ||||  ||||||||||||||||||||||| || |||||||| |||||    || ||||  || |  |||
gttagttcttactacctgaaaattgtgcagtcactgtaatttatattgcctatgtaa-attgtgcagtcactgtaataggagcaa---tgggcctgttttggttgtttatttcggaagcttaatcctatcattctgagtgcagGAGCAACTCTAGCCTGTGGAACTGGAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGG
















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|162269245|gb|FC445802.1|FC445802
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|37834821|gb|BJ592833.1|BJ592833
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|37835319|gb|BJ593331.1|BJ593331
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162186404|gb|FC362960.1|FC362960
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162252751|gb|FC428788.1|FC428788
EST:     GGTCTTCTTTGGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTATTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|67700556|gb|BJ960789.1|BJ960789
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162232388|gb|FC408822.1|FC408822
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162186405|gb|FC362961.1|FC362961
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|22132121|gb|BQ826991.1|BQ826991
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|22491789|gb|BU051712.1|BU051712
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|37834965|gb|BJ592977.1|BJ592977
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162243414|gb|FC425110.1|FC425110
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|67726581|gb|BJ976840.1|BJ976840
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162269244|gb|FC445801.1|FC445801
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|37849296|gb|BJ607304.1|BJ607304
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|37841391|gb|BJ599399.1|BJ599399
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162252752|gb|FC428789.1|FC428789
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|37827317|gb|BJ585329.1|BJ585329
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162233272|gb|FC409614.1|FC409614
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162243413|gb|FC425109.1|FC425109
EST:     GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
EST: gi|162169969|gb|FC345909.1|FC345909
EST:     GGTCTTCTTTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCG                         GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG
genomic: GGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAG

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: 31 (upstream exon), 34 (downstream exon)
Score: 23

AGTTTGTTGAGGTCTTCTCTCGTAATCACCTCAAAATGCGCGTGTGGGAACGGGGCGCCGgtatggcttt ... tcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacctcagcctgctactatcacttgattaatcttgtttgtcttttcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG
                         gattaat  putative branch site (score: 23)
                               tcttgtttgtcttttc  CT-rich tract
                       ttgattaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcttgttggcctttccatcattgtctagtacatgttatagatctcaacctcagcctgctactatcacttgattaatcttgtttgtcttttcatggacagGTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA