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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactggtcaactttcattttttttttttttcattctcgcatgacattgtagaaaattatgacagtgtaatttcatcttatatattcttttgttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG

Basic information

species Vitis vinifera
transcript Vv04s0023g03620.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 5
gtaactggtcaactttcattttttttttttttcattctcgcatgacattgtagaaaattatgacagtgtaatttcatcttatatattcttttg-ttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG
           | ||       ||||| || | |  ||   | || | | |   || ||  |||  |      |  |||| || |||||||     |||    ||  ||||||||| || || || || || ||||||||||||||||||||||||||||||||||| || ||||||||||| || |||||  |||| ||||| |||||||| 
-----------aattctgcccatttttcttctaaccctgaaaggagagtttg--aactttggactcttgtgcattttcttttaaattctttgaaccttggactcttgtggcagTACTCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCTGCTGCAGCAGCAGCAGGCGGTGTATCTGGATTTGAGTTTGGTGTT

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G36990.1 (Glycine max), 3'ss of exon 5
-gtaactggtcaactttcat--tttttttttttttcattctcgcatgacattgtag-aaaattatgacagtgtaatttc----atcttatat--attcttttgttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG
  |    ||   | ||||||  | | |||||| ||  || || | ||    | |   || || |   || ||||| ||     |||| || |  ||  |  ||   |||| | |  |||||||||||| || ||||| || ||||||||||||||||||||||||||||| ||||| || || || ||||||||||||||  | || ||||| ||||| |||
gttcgtgggctcaatttcatcgtgtgttttttcttttttgtcccttgtttctctcttaagataagttcaatgtaacttttttgatctaattttgatattcatgcgatgttgctttctggcagTACACCTATTTTCACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCAGCTGCTGCTGCTGCCGCTGCAGCTGGTGGTGTATCAGGATTTGAGTTTGGCGTG

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 5
----------------gtaactggtcaactttcattttttttttttttcattctcgcatgacattgtagaaaattatgacagtgtaatttcatcttatatattcttttgttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG
                  | ||  |    |||   | | ||| ||||| || ||    |    |  ||  | |   | |   | |  ||   ||||| | ||  |  ||| ||||| | |  ||||||||| || || || || || |||||||||||||||||||||||||| || ||||||||| | || ||||||||||||||  | || ||||| ||||| |||
gtttgtgggcttaatttcatcttcttttttttttctctctttcttttttatcctttgtttctctcttaatataagttcaatctatgtttctctctta-agatattcatgtgttgttgctttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGCTGCCGCCACCGCTGCAGCTGGTGGTGTATCCGGATTTGAGTTTGGCGTG

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 5
gtaactggtcaactttcattttttttttttttcattctcgcatgacattgtagaaaattatgacagtgtaatttcatcttatatattcttttgttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG
             | | | |||   || |  |  ||    | || | |  | | |||| || |   | |  | ||| |   | | |   |   || || || |||   ||||| |  | ||||| || || ||||| |||||||||||||| ||||| |||||||| |||||| | || || |  | ||  | ||||  ||    |||||  
---------atgatcttactttgaattctgatggtttgtac-tggcctcttggtaaatgat-atgttttggtatcacca-gtctctctctaatttatggttactccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA

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|110724206|gb|EE099841.1|EE099841
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGGAAAGTGGAAGTGGTTTTGCACCAG
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGG-AAGGTGGAAGTGGTTTTGCAGCAG
EST: gi|110718273|gb|EE094914.1|EE094914
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAAGGTTGGAAGTGGTTTTGCAGCA
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAA-GGT-GGAAGTGGTTTTGCAGCA
EST: gi|110425434|gb|EC991819.1|EC991819
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|110721698|gb|EE098992.1|EE098992
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGATGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|110723511|gb|EE100909.1|EE100909
EST:     ATAGTCCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|110684657|gb|EE062188.1|EE062188
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|110693944|gb|EE070616.1|EE070616
EST:     CTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: CTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|110702751|gb|EE079006.1|EE079006
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGATGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAAGTGGAAGTGGTTTTGCAGCAGC
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|110384926|gb|EC949397.1|EC949397
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|110687737|gb|EE065489.1|EE065489
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|110689406|gb|EE065602.1|EE065602
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGC
EST: gi|110730475|gb|EE107599.1|EE107599
EST:     ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAG                         TACACCCATCTTCACAGGGGATGGGGGAAGGTGGAATTGNTTTTGCANCAN
genomic: ATAGTTCATGTTCCTGCTGGTCCAAATGCTCTTTCTGACGTGCTTATAAGgtaactggtc ... ctcatggcagTACACCCATCTTCACAGGGGATGGGG-AAGGTGGAAGTGGTTTTGCAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgacagtgtaatttcatcttatatattcttttgttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG
                          tattcttttgttttgt  CT-rich tract
           taatttcatcttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactggtcaactttcattttttttttttttcattctcgcatgacattgtagaaaattatgacagtgtaatttcatcttatatattcttttgttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG