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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatctattaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC

Basic information

species Vitis vinifera
transcript Vv17s0000g00500.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 4
gtatgtttttttcttcgccc--cctttttcctcaaggtagtccgttttcatgaacatgggtatctattaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
|||||  |   |  | | |   | |||||  | || | | | |  | |  |   ||    |    |||   |  |   | |   | ||||||| || | | | || |  ||  ||||||| |  ||||||  ||||||||||||||||||||| ||  | ||||||||||| ||||| |||||||| ||
gtatgcctggatgcttgtcatgcttttttttttaaagaactgcagtct-gtaggcacca-tgctgattcctttta---tttggcaacagGCACGACCAAACTTCACACTGAGTTGGAGGAGTTGGTTGCACGCTTTGTTGGAAAGCCTGCTGCTATCCTATTTGGCATGGGTTATGTTACAAACTCGGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 3'ss of exon 4
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatg---ggtatcta---ttaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
||| |   || | ||    |  |  ||  |       |     ||  ||||    |    |||| ||   ||| || |   ||| |   | ||||| ||| |   |||||   ||| | || ||    |||||||  |||||||| |||||||| || ||  | ||||||||||| |||||||| ||||||||
gtaggcacttatgttgctgctatagtttgttgccactgagttcttaaatgatttagtgtagtatataagcttacctgattcatacaatcttagGCAACACTAAGCTGCATGTGGAACTTGAAGAGCTGGTTGCAAGATTTGTTGGCAAGCCTGCAGCTATTCTTTTTGGCATGGGTTATGTGACGAACTCTGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 4
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatctattaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
||||| |   ||||   |   ||| |   |  |   |     |||| | ||||||  |   ||  |  ||   |  | | ||| |||| || || |   | || |  ||  ||||||| |    ||||   |||||||||||||||||||| ||  ||||||||||||| ||||| |||||||||||
gtatgctacattctcaacatgcttatattttta--caac---tttttaggaacataag---ctgatccctttcatct-tgtga-cagGTACGACCAAGCTTCACACTGAGCTGGAGGAGTTGACTGCACGTTTTGTTGGAAAGCCTGCTGCTATCCTCTTTGGCATGGGTTATGTTACAAACTCTGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 4
--------gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatg--ggtatctatta-----actaaaaaatatatga--tcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
         ||||||| |      |   |   |||     |||| |   | |||||  || ||      ||   |||     | | |    ||| |||  | |||||  || |  ||||| | |||  | || ||   ||||||||  |||||||| |||||||| || ||  | |||||||||||||||||||||||||||||
gtcggtgcttatgtttatcaaactgtgtcacgttttacgtaggttgagtggtttcagtaatatatcaaaattcgttagactgattgagttttatctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTGGTAAGCCTGCAGCTATTCTTTTTGGCATGGGCTATGTGACAAACTCTGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 3
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatctattaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
||| | |   || |   |   ||  |   |  |   | |   |    |  || |   |||  | | | |      || |   |||||| |  || |  || || || ||  | ||||| |    |||    |||||||||||||||||||| ||  | ||||||||||| ||||| |||||||||||
gtaggatacattatcaacatgctcatatgtttaca-actttttaagaacaaaaactagtaaat-tgatcccttttatctcgtatcagGTATGACCAAGTTTCACAATGAGCTAGAGGAGTTGCCTGCGCGTTTTGTTGGAAAGCCTGCTGCTATCCTATTTGGCATGGGTTATGTTACAAACTCTGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 4
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatcta---ttaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
||| | |   ||||   |   ||| |   |  |   |     |||| | |||||       |||   | | |      ||||   |||||| || || |   | || || ||  ||||||| |  | |||    |||||||||||||||||||| ||  | ||||||||||| ||||| |||||||||||
gtaggatacattctcaacatgcttatatgtttacaaa-----tttttaagaacaaaaactactaaactgatccctttcatatcgtatcagGTACGACCAAGCTTCACAATGAGCTGGAGGAGTTGGCTGCGCGTTTTGTTGGAAAGCCTGCTGCTATCCTATTTGGCATGGGTTATGTTACAAACTCTGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G067257_T01 (Zea mays), 3'ss of exon 6
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatcta---ttaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
||| | |   || |   |   ||| |     | | |      |||| | |||||       |||   | | |      || |   |||||| || || |  || || || ||  | ||||| |    |||    |||||||||||||||||||| ||  | ||||||||||| ||||| |||||||||||
gtaggatacattatcaacatgcttat-----atgtttacaactttttaagaacaaaaactactaaactgatccctttcatctcgtatcagGTACGACCAAGTTTCACAATGAGCTAGAGGAGTTGCCTGCGCGTTTTGTTGGAAAGCCTGCTGCTATCCTATTTGGCATGGGTTATGTTACAAACTCTGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G055854_T01 (Zea mays), 3'ss of exon 2
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatcta---ttaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
||| | |   || |   |   ||| |     | | |      |||| | |||||       |||   | | |      || |   || ||| || || |   | || || ||  ||||||| |    |||    |||||||||||||||||||| ||  | ||||||||| | ||||| |||||||||||
gtaggatacattatcaacatgcttat-----atgtttacaactttttaagaacaaaaactactaaattgatccctttcatctcgtattagGTACGACCAAGCTTCACAATGAGCTGGAGGAGTTGCCTGCGCGTTTTGTTGGAAAGCCTGCTGCTATCCTATTTGGCATGTGTTATGTTACAAACTCTGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G357734_T02 (Zea mays), 3'ss of exon 8
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatcta---ttaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
||| | |   || |   |   ||| |     | | |      |||| | |||||       |||   | | |      || |   |||||| || || |  || || || ||  | ||||| |    |||    ||||||||||||| |||||| ||  | ||||||||||| ||||| |||||||||||
gtaggatacattatcaacatgcttat-----atgtttacaactttttaagaacaaaaactactaaactgatccctttcatctcgtatcagGTACGACCAAGTTTCACAATGAGCTAGAGGAGTTGCCTGCGCGTTTTGTTGGAAAGCTTGCTGCTATCCTATTTGGCATGGGTTATGTTACAAACTCTGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G370377_T01 (Zea mays), 3'ss of exon 9
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatcta---ttaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
||| | |   || |   |   ||| |     | | |      |||| | |||||       |||   | | |      || |   || ||| || || |   | || || ||  ||||||| |    |||    |||||||||||||||||||| ||  | ||||||||| | ||||| |||||||||||
gtaggatacattatcaacatgcttat-----atgtttacaactttttaagaacaaaaactactaaactaatccctttcatctcgtattagGTACGACCAAGCTTCACAATGAGCTGGAGGAGTTGCCTGCGCGTTTTGTTGGAAAGCCTGCTGCTATCCTATTTGGCATGTGTTATGTTACAAACTCTGC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G23670.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatctattaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
             |       ||||  |   |   |         |  ||    ||  | |  |  ||||      | |   |||||| || ||| |  |||||  |||| | |||||||||||| | |  ||||| ||||||||||||||  | || ||||||||||||||||  ||||| || ||
------------gtaaagtgtctttgcctatagattcaagaaccattttggctctgtttctaaacaaacttttt--tctgctatcagGAACTACATCCGTGCATGCAGAACTTGAGGAATGTGTTACTAGGTTTGTGGGAAAGCCTGCTGCTGTTGTTTTTGGCATGGGCTATGCAACAAATTCGGC

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|71854830|gb|DT003885.1|DT003885
EST:     GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAG                         GCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
genomic: GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAGgtatgttttt ... atatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
EST: gi|34542640|gb|CF510872.1|CF510872
EST:     GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAG                         GCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
genomic: GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAGgtatgttttt ... atatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
EST: gi|71874609|gb|DT023664.1|DT023664
EST:     GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAG                         GCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
genomic: GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAGgtatgttttt ... atatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
EST: gi|110709258|gb|EE084571.1|EE084571
EST:     GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAG                         GCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
genomic: GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAGgtatgttttt ... atatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
EST: gi|71864618|gb|DT013673.1|DT013673
EST:     GTCTTTGAAGAAGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAG                         GCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
genomic: GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAGgtatgttttt ... atatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
EST: gi|71861348|gb|DT010403.1|DT010403
EST:     GTCTTTGAAGAAGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAG                         GCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
genomic: GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAGgtatgttttt ... atatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
EST: gi|71867645|gb|DT016700.1|DT016700
EST:     GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAG                         GCACCACAACATTGCATAAAGAAGTGAAGGAATGTGTTGCAAACTTTGTTG
genomic: GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAGgtatgttttt ... atatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
EST: gi|161718030|gb|FC068557.1|FC068557
EST:     GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAG                         GCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGT
genomic: GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAGgtatgttttt ... atatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGT
EST: gi|161717233|gb|FC067239.1|FC067239
EST:     GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAG                         GCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG
genomic: GTCTTTGAAGAGGTTTTCCCCAGGTACCTGTAGCACCCGTGTTGATGGAGgtatgttttt ... atatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtagtccgttttcatgaacatgggtatctattaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC
                          tatctattaactaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatgggtatctattaactaaaaaatatatgatcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC