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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC

Basic information

species Vitis vinifera
transcript Vv05s0094g01380.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 2
gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccat-tttcatattcatgcttctgaaattcctatgatt-atttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
                                              |  || | |  ||| |  |     |  | |  ||  | || ||| ||     | || ||  ||||  ||| |||  ||  || |||||||| || || || ||||| || || ||||| |||||||||||||||||| | |||||  |||| || || || |||||| |||| |||||||| ||||
----------------------------------------------gtatg-tcacagagtcttatggtataatagttcttccaatatttgattcatgtactactctaattaatattatttgttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G022090_T02 (Zea mays), 3'ss of exon 1
gtatgatgctgta-acttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctcca-ttttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
||||| | || |   ||  | ||| |  || | || ||    ||| |   |||  | || |    | ||| |  |    |  || |   ||  || | ||| || ||       ||| |||      | |||||||| || || |||||||| || || ||||| || ||||||||||||||||| ||||| |||||||| || ||||||||||||||||||||||| ||||
gtatgttcctatgtgctgttgtca-tccatatgatctccctgatt-tatatgcc-agtgtgttttatatgatcttatatccttctagcattgttaataatgtttgtg-------tataatt------tgcagAAAAATCATATATTTACATCTGGTGCTTCTGGAACAAATGCAGCTGTTATCAGGGGTGCTCTAAGAGCTGAAAAACCAGAGCTGCTTACTGTAATTTTAC

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
||| | | || |      |    ||  || | || ||    ||| |   |||   |   |  ||  ||  |  | |  | ||| |  ||  || | ||| || ||       ||| |||      | |||||||| || || || ||||| || || ||||| || |||||||||||||| || || ||  ||||||| || || |||||| ||||||||||||| ||||
gtaggttcctatgtgccattgtcgttcatatgatctccctgatt-tatatgccagtgtggttca-tattatctttgatccctctagcttgttaataatgtttgtg-------tataatt------tgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 3
gtatgatgctgtaacttctatcagta-tattttatgtct------aacattgtggg------tgcttattgagcccaacatgctgc-----tgggactct------ccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
||| | | |||| | ||   ||  || |||  ||||  |      |   ||||||       |   |  |||       |||| |      |  || | |      | |||   |||    ||  ||  || ||| | |   | | |  |  ||||||| || || |  ||||| ||||||||||| |||||||| ||||||||| |||||||  |||| ||||||||||| ||| |||||||||| || ||||
gtaagtttctgttattttactctatagtatcatatgctttcttgtagtcttgtggaacacaatatatggtgaattggtgatgcagtatagttatgatttttgttaacaattccaatagctgtgtctcacaacttcttgtccatctgtt-tgtagAAAAATCATATATACACATCTGGAGCATCTGGGACTAATGCTGCTGTTATCCGAGGTGCTTTAAGGGCAGAGAAACCGGAGTTGCTTACTGTTATATTAC

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G00330.1 (Glycine max), 3'ss of exon 3
-----------------------gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaaca-tgctgctgggactctccattttcatattca-----tgcttctgaaattcctatgattattt-cctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
                       |||| ||    |  |||  |    |  | | | |||  ||||   |   || | | |  |     || | ||  |     | |   ||  ||  | ||     ||  ||| | |      ||   || |   |  ||||||| || || | |||||| ||||||||||| |||||||| ||||||||  |||||||  |||| ||||||||||||||| ||||||| || || ||||
gtaagttgttattttactcaagagtattatatgcttgcttgaagagtttcagtct-tgtagaacacaatatatggtgaattggtgatgcagtactagttatgatttttgttaacaactccaatggctgtgtctcacaacttcttgtccatctgtttgtagAAAAATCATATATATACATCTGGAGCATCTGGGACTAATGCTGCTGTTATTCGAGGTGCTTTAAGGGCAGAGAAACCAGAGTTGCTTACAGTTATATTAC

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G59870.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
                      |  | |||||   |  ||   |        ||  ||| ||  | ||| |  |||  | |  ||| || |||  ||| || |       ||| ||||| | || | ||||||||||| || |  |||||||| ||| |||| || |||||||||||||| |||||||| || |||||||||| ||||||||| ||||| || |||||||
--------------------gtaagacattttgcctacaaggctacaa----tttctgaacc--atatgtt--tggttcaccacatctt-ataaccat-ctcc-------cctgtgatt-tatcttgcagAAAAACCATATCTACACATCAGGTGCAGCTGGAACCAATGCAGCTGTTATAAGAGGTGCACTTAGAGCAGAGAGACCAGAGCTTCTTACAGTTATCTTAC

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
                                            ||  ||  |||  || |   |    ||  ||     ||||  |    |    |    |||  |||   |  |    |||| | |||||||| || || |  |||||||| |||||||| |||||||| || || |||||||||||  | |||||||||| ||||||||||||||| |||||  |||
--------------------------------------------gtaagtcatta--gaacttcatcctcttgtgtttgactccgatccatttaaaacatctctcgaataattcgg----tttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S323_60V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatgatgctgtaacttctatcagtatattttatgtc-taacattgtgggtgcttattgagcccaacatgctgctgggactctccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
             |     |||||  | | |  |||| | | || ||     |      ||    |||  || ||   |||   || |   | |  |||  ||    || || | |  |  |||     ||||||| ||||||| ||||||||||||| | || || || ||||||||||| || || ||  | ||||| || | |||||| || |||||||||||  |||
-------------atacgaatcagagt-tctactgtcatgatatcgtaatcac------agtttcacaaccttcttcaact--tcagtgctagac-catattt----aactcttctcttcgtttt----agAAAAATCACATTTATACATCAGGAGCAGCGGGAACAAACGCAGCTGTTATAAGGGGAGCATTGAGAGCTGAAAGACCAGACCTCCTTACTGTAATTCTAC

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|18459061|gb|BM437339.1|BM437339
EST:     TCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTAT-G--------                         AAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC
genomic: TCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTATGGTTATAACTgtatgatgct ... tttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC
EST: gi|71870474|gb|DT019529.1|DT019529
EST:     TCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTATGGTTATAACT                         AAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC
genomic: TCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTATGGTTATAACTgtatgatgct ... tttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC
EST: gi|30320624|gb|CD003886.1|CD003886
EST:     TCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTAT-G--------                         AAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC
genomic: TCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTATGGTTATAACTgtatgatgct ... tttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC
EST: gi|30321162|gb|CD004424.1|CD004424
EST:     TCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTAT-G--------                         AAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC
genomic: TCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTATGGTTATAACTgtatgatgct ... tttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC
EST: gi|110374681|gb|EC939602.1|EC939602
EST:     TCACACATCAAGAACTTATTGAGATTTTCAGCTATGCTATGGTTATAACT                         AAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC
genomic: TCACACATCAAGAACTTATTGAGATTCTCAGCTATGCTATGGTTATAACTgtatgatgct ... tttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactctccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
                                          ttatttcct  CT-rich tract
         attttcatattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT