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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC

Basic information

species Vitis vinifera
transcript Vv07s0005g00770.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 13
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC
  |||   | |  | |   | || | | |||| | ||| |                 ||||    |   ||||||  ||| | ||| | |       |||||| || |||| || ||||||||||||||||||||||| || |||||||| || ||||| || || ||||||||| | ||||| ||||| |   |||||||||
--gtgagttatcttcttttcgtcatattaaatgttcttttg--------------tgaaatatacaacctttctaacaatta-attgtgt-------caacagGTGGAAGATTACATTGCAACTCCAAAACCTAATGGGTACCAAAGTCTACACACAACAGTGATACCATTTCTTAACGAGAGTATGTTCCATTTGGAAGTTC

upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G416698_T01 (Zea mays), 3'ss of exon 7
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC-
                |    |  | |    ||||  ||  ||||||   ||       |   | | ||||      || |||   |||| ||     ||||| || |||| || |||||||||||||||||||||||||| ||||| || || ||||| || || |||||| || ||||||| |||||||   ||||||||| 
----------------gtgagttatcttctttttg--tcgtatttaatgttcttttgtgaattccacttttct----aacaatcagttatgtt-----aacagGTGGAAGATTACATTGCAACTCCAAAACCTAATGGCTACCAAAGCCTACACACAACAGTGATACCATTT-TTAATGAGAGTATGTTTCATTTGGAAGTTCA

upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G416698_T02 (Zea mays), 3'ss of exon 6
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgac-tagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC
 | || ||    | || | ||  || |||  | | |||||  ||   ||||   |     |    |   ||         ||| | |   || | ||  ||||| || |||| || |||||||||||||||||||||||||| ||||| || || ||||| || || |||||| || ||||||                     
atatggacacc-cgttcctcaagctgtgagttat-cttctttttgtcgtatttaatgttcttttgtgaattccacttttctaacaatcagttatgtt--aacagGTGGAAGATTACATTGCAACTCCAAAACCTAATGGCTACCAAAGCCTACACACAACAGTGATACCATTT-TTAATGAGA---------------------

upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 16
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttattt-ttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC
||  |||  ||  |||  |     ||||| | | |    |  |     ||  ||||| ||    |  ||           |||||||  ||| |||||    || |||| || ||||||||||| || ||||| |||||||| || ||||| || || ||||| ||||||||| | ||||||||||||||| | || ||||| |
gtacgtatgttattttctattatatttgagagtagaaagtgttagttttaagagacataaattttcattgactggtgtggaatatttggtttgttttgttttagGTGAAGGATTATATTGCAACCCCTAAACCAAATGGCTACCAGAGTCTTCAGACCACTGTGATTCCATTTTTGTATGAGAGCATGTTTAGGCTAGAAGTCC

upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 14
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttattt-ttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC
|| ||||   |  |||  |     ||||| | | |    |  |     ||  ||||| ||    |  ||        |  ||||||| |||| |||||    || |||| || ||||||||||| || ||||| |||||||| || ||||| || || || || ||||||||| | ||||||||||||||| | || ||||| |
gtatgtatgctattttctattatatttgacagtagaaagtgttagttttaagagacataaattttcattgactggtgaggaatatttgatttgttttgttttagGTGAAGGATTATATTGCAACCCCTAAACCAAATGGCTACCAGAGTCTTCAGACCACCGTGATTCCATTTTTGTATGAGAGCATGTTTAGGCTAGAAGTCC

upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT4G02260.3 (Arabidopsis thaliana), 3'ss of exon 14
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC
                               | ||  ||  || |   | | |  ||   |   ||  || |||| |  |   | |  |  | | |   |||| | ||||| || |||||||| || || || ||||| || || || |||||||| ||||| ||||||||  | |||||||| |||||||||||||| ||||
------------------------------gtatgtatcagatcttt-tgttattcaggtta--tatcttatctacat-tgggactgaacatatgtcttacagGTAAAAGATTACATTGCAACCCCGAAGCCCAATGGATACCAGAGCCTCCATACTACTGTGATTCCATTCTTGTATGAGAGTATGTTTCGACTGGAGGTTC

upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S194_9V6.1 (Physcomitrella patens), 3'ss of exon 13
--------gtgtgtactttgctttg-cacatcctt----tgaaatttgcttctaatttaa---gtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGAC-TGGAAGTTC
         |    |||| | | ||  ||| || |    || | ||  |||    ||| |   ||  |  |||   ||      | |  |   | | |   || | |||       |||||||||||||| ||||| || ||||| |||||||| ||||||||| | || || || || |||||||| |   |      | |  |||  | | ||| |||
gtgcgcagatcctaacttcgttgtggtacacccatgaggtgcatttaactttatgttttatccgttccttacagtttgcaatagtgtcgtgtgacttaggcttcactttggctgtgcagATGAAAGACTACATTGCTACACCAAAGCCTAATGGTTATCAAAGTTTGCACACCACAGTTATTCCATT-CGGCACACAGACTTACTTCCCCATCGAAATTC

upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S195_4V6.1 (Physcomitrella patens), 3'ss of exon 14
------------------------------------------gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC
                                            ||| |  | || ||       |||   |||| | ||  || ||  || |  | |  | |     |  |   | ||     |        | | | || |||||||| || |||||||| |||||||| || || |||||||||||||| ||||| || || ||||||||        |||     ||||  |||||| |||
gtgcgcagcttcttacctcatcacagtatcgtattgtatactaggtgcatatggccttttggtctctt---aattggtttgcaacttgtgtttttgccctattcttctgactccattgatgggttgaacccgctctcttca-cagATGAAGGATTATATTGCTACTCCAAAGCCGAACGGCTATCAAAGTCTGCATACCACAGTCATTCCATTCGGCACACAGACTTACTTTCCTCTGGAAATTC

upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ30490 (Selaginella moellendorffii), 3'ss of exon 11
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC
                                                         || |   |  || |  |   | | | | || |  ||  |||  |||||||||||||| ||||| || |||||||| |||||||| |||||||| || || |  || || ||||||  ||   |||   | || | ||||||| |||
-------------------------------------------------------gtaagtttttctttgtaatgccactga-acttaaaattcgtgct-cagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCACTGGAAATTC

upper sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ23048 (Selaginella moellendorffii), 3'ss of exon 11
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC
                                                         || |   |  || |  |   | | | | || |  ||  |||  |||||||||||||| ||||| || |||||||| |||||||| |||||||| || || |  || || ||||||  ||   |||   | || |  |||||| |||
-------------------------------------------------------gtaagtttttctttgtaatgccactga-acttaaaattcgtgct-cagATGAAAGACTACATTGCTACCCCAAAACCCAATGGCTACCAAAGTCTACACACTAAAGTCATCCCATTTGGTTCAAAGACATTTTTCCCGCTGGAAATTC

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|352772776|gb|FQ473814.1|FQ473814
EST:     ACCATGTTCTTGGGTTGGTCCATGGAATCTGGACTCCTGTTCCGCGAGCT                         ATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCAT
genomic: ACCATGTTCTTGGGTTGGTCCATGGAATCTGGACTCCTGTTCCGCGAGCTgtgtgtactt ... tttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC
                                  tattttattttttt  CT-rich tract
        aaaatgactagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG