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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctttatttatctaaaatctcagaatcatctgttagggttaaaacaaccctcatgatgtgggataattccatcaaattacttctctgaaaatcgtttctgtttatatgttcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAGTGCATCGGTGCTGCTGCATAAGTGTACCAAATCTTGATAAAAATCTCTG

Basic information

species Vitis vinifera
transcript Vv01s0127g00260.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G17010.2 (Glycine max), 3'ss of exon 11
gtatatctttatttatctaa--aatctcagaatcatctgttagggttaaaacaaccctcatgatgtgggataattccatcaaattacttctctgaaaatcgtttctgtttatatgttcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAGTGCATCGGTGCTGCTGCATAAGTGTACCAAATCTTGATAAAAATCTCTG-
|||| || |||| || | || ||| |||| | | | | | | |||| | | |||| | | || | || || ||||||||||||||||||||||||||| |||||||| ||||||||||||||||| | |||||| ||||||||| ||| | | ||| | | || || |
-------gttatataactaactgattcctttattgattgt----attaacaaaccatctaaaccgatgctcaattttctttaggaactttctctgatctagtatttg-------gtctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAATGCATCACTGCTGCTGCTTAATTAT-CCATTCTTAGGCCAATCCCTTTTT

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA15G42140.2 (Glycine max), 3'ss of exon 11
gtatatctttatttatctaaaatctcagaatcatctgttagggttaaaacaaccctcatgatgtgggataattccatcaaattacttctctgaaaatcgtttc-tgtttatat--gttcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAGTGCATCGGTGCTGCTGCATAAGTGTACCAAATCTTGATAAAAATCTCTG-
|||| || |||| || | | | | | | || || || || || || | || | |||||| || ||| | | | | | ||| | || ||||||||||||||||||||||||||| |||||||| ||||||||||||||||| | | |||| ||||||||| ||| | | ||| | | || ||
-------gttatataactaa---ctgatttccttttatgattgtgttaagaaacc-----atctgaactgatacttacaaatttttttaaggaacgttttatgatatatattttggtctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAATACATCACTGCTGCTGCTTAATTAT-CCATTCTTAGGCCAATGCCTTCTA

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA01G03530.1 (Glycine max), 3'ss of exon 12
gtatatctttatttatctaaaatctcagaatcatctgttagggttaaaacaacc--ctcatgatgt-gggataattccatcaaattacttctctgaaaatcgtttctgtttatatgt-tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAGTGCATCGGTGCTGCTGCATAAGTGTACCAA-ATCTTGATAAAAATCTCTG
|| | | | || | || | | || || || ||||| | ||| ||| ||| |||| | | | ||| || ||| || |||| | | | |||||||||||||||||||||| || || |||||||| ||||||||| ||||||| ||| ||| |||||| || |||| | ||| | ||| || | | |
--gtaacccaactcatgcctttattattgattgtattgaagtattgaa-caaccaattgatgctgttaggaaaattttccctgaggaacagtctttaatc--tttttggttatctatcttttttacagGTTTATGGACCTGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAGTTCATTACTGCTGCCGCTTAAGGTCAACAACACCTTCATTTATAGTATT-

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 12
gtatatctttatttatctaaaatctcagaatcatctgttagggttaaaacaacc--ctcatgatgt--gggataattccatcaaattacttctctgaaaatcgtttctgtttatatgt-tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAGTGCATCGGTGCTGCTGCATAAGTGTACCAA-ATCTTGATAAAAATCTCTG
|| | | ||| || | || | | || || || | ||| | ||| ||| || ||| || | | | || | || ||| || |||| | | | ||||| ||||||||||||| || || || |||||||| ||||||||| ||||||| ||| ||| || ||||| |||| | ||| | ||| || | | |
--gtaacctaattcatgcctttattattgattgtattgaagtattgaa-cgaccaatttatgctgtttggaatatttgccttgaggaacaatctttaa---tctttttggttatctatcttttttatagGTTTATGGACCCGAAGCCACAATGACTGGTATATGCAAAGAGGCAATACAGTTCATTACAGCCGCTGCTTAAGGTCAACAACACCTTCATTTATAGTATT-

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|110363218|gb|EC926793.1|EC926793
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGGCCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|111125104|gb|EE253722.1|EE253722
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCCGAGGCAACCATGACTGGCATATGCAAACAGGCGATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|32247604|gb|CD713423.1|CD713423
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGGCCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|71888760|gb|DT037815.1|DT037815
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGGCCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|30325227|gb|CD008489.1|CD008489
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGGCCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|110698225|gb|EE075525.1|EE075525
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|349820930|gb|FQ408638.1|FQ408638
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|110702653|gb|EE078810.1|EE078810
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|32271862|gb|CD721021.1|CD721021
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGGCCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|351035742|gb|FQ463587.1|FQ463587
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|32271741|gb|CD720900.1|CD720900
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGGCCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|110389062|gb|EC953874.1|EC953874
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|110421990|gb|EC988298.1|EC988298
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGGCCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|110416323|gb|EC982295.1|EC982295
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGGCCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|110422467|gb|EC988792.1|EC988792
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|32272154|gb|CD721313.1|CD721313
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGGCCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|110422525|gb|EC988850.1|EC988850
EST:     AAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: AAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|71882170|gb|DT031225.1|DT031225
EST:     GTCTTGCAAAAATGCGAACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCT
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCT
EST: gi|46910213|gb|CN545588.1|CN545588
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
EST: gi|351044803|gb|FQ449057.1|FQ449057
EST:     GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAG                         GTT-ATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG
genomic: GTCTTGCAAAAATGCGGACTCTTGGAGAGGAAATTGGAATCCCTCTTGAGgtatatcttt ... tcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattccatcaaattacttctctgaaaatcgtttctgtttatatgttcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAGTGCATCGGTGCTGCTGCATAAGTGTACCAAATCTTGATAAAAATCTCTG
                                          tgttctttt  CT-rich tract
 tttatatgttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatctttatttatctaaaatctcagaatcatctgttagggttaaaacaaccctcatgatgtgggataattccatcaaattacttctctgaaaatcgtttctgtttatatgttcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAGTGCATCGGTGCTGCTGCATAAGTGTACCAAATCTTGATAAAAATCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC