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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctttttctgtattggtttgatttatagcttctttgtgatgattgtttagttcattttaatggtctatgtgggctgatttgggattttttggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG

Basic information

species Vitis vinifera
transcript Vv01s0010g02460.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g40950.1 (Oryza sativa), 3'ss of exon 5
-ctctttttctgtattggtttgatttatagcttctttgtgatgattgtttagttcatttta---atggtctatgtgggctgatttgggattttttggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG
    ||| |  | |          | || | ||  ||||| ||       | ||||| | |   ||| |     |||  | || || |   |||   |    |||||||||| ||||||||  |||||||||| |||||||| ||||| |||||||||||| | ||||||||||||||||| |||||||| || ||||||||||
gtattttctgcgaaacccaacatgtcattgtttgattgtggtgtcataacaattcatatgaagaatgattctcatggtatcatatgcg---tttcaata--tagGGTGGTGCTAAGAAGGTCGTCATCTCTGCTCCCAGCAAGGATGCCCCCATGTTTGTTGTTGGTGTCAATGAGAAGGAGTACAAGCCTGACATCGACATTG

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g38920.1 (Oryza sativa), 3'ss of exon 5
ctctttttctgtattggtttgatttatagcttctttgtgatgattgtttagttcattttaatggtctatgtgggctgatttgggattttttggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG
                          ||  ||| | |||   ||| ||  |||||   | | | | ||  |  | |   |      |||||  |  |||||||||||| ||||||||  |||| ||||| ||||||||||| || |||||||| ||| | |||||||| |||||||| |||||| | ||  |  ||||||
-------------------------gtacattcct-gtgtcaatttttctgttcagggtcaagctgtagatctgtt--ctcaatcatttttcatatgcagGGTGGTGCCAAGAAGGTCGTCATTTCTGCTCCCAGCAAAGACGCCCCCATGTTCGTTGTTGGTGTCAACGAGAAGGAGTACAAGTCTGACGTTAACATTG

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g03290.3 (Oryza sativa), 3'ss of exon 4
---ctctttttctgtattg-gtttgatttatagcttctttgtgatgattgtttagttcattttaatggtctatgtgggctgatttgggattttttggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG
    | ||  |||| |  |   ||| | |  | || | ||||    ||   |||| | ||||   ||   | | |  ||| |  |||   | ||  |  | ||||||||||| ||||||||  ||||||||||||| |||||||||||||| ||||||||    |||||||| ||| |  | ||||   | ||||| || ||||
ttatttttactctgaaaagtacttgttgtgcatctcccttgttgc-ataagttagct-atttcggtgcattttttatgcttacatgg--ctgttctgaaaacagGGTGGTGCCAAGAAGGTTGTCATCTCTGCCCCGAGCAAAGATGCTCCGATGTTTGTCTGCGGTGTCAACGAGGACAAGTACACTTCAGATATTGATATTG

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G180625_T02 (Zea mays), 3'ss of exon 5
ctctttttctgtattggtt--tgatttatagcttctttgtgatgattgtttagttcattttaatggtctatgtgggctgatttgggatttt-ttggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG
 |  |    |||  ||| |  ||| || |  ||||  | | |   |  ||| ||    |  |||||    |   |   | |||    |  | |||     ||||||||||| ||||||||  | ||||||||||| ||||||||||| |||||||||||| | |||||||||||| |  | ||||   ||||| |  ||||||
-tagtgcagtgtcatggctcatgacttgtcacttcacttttactgtattttcgtctgct--aatggatgtttctgatagctttattttcctattgaatgacagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCAAGCAAAGATGCGCCCATGTTTGTTGTTGGTGTCAATGAGGACAAGTACACCTCCGATGTTAACATTG

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G046804_T02 (Zea mays), 3'ss of exon 5
ctctttttctgtattggtttgatttatagcttctttgtgatgattgtttagttcattttaatggtctatgtgggctgatttgggatt-ttttggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG
||| ||     |||    |  | || ||  || | |  |||     |||  |   ||  | |||    |   |   | |||    |  |||||     ||||||||||| ||||||||  | ||||||||||| |||||||| || |||||||||||| | |||||||||||| |  | ||||   | ||| |  ||||||
ctcgttactcttatcacatc-acttctactttgtgtcagattggattttcctctgttaaattggatgtttctgatagctttactttccttttgaatgacagGGTGGTGCCAAGAAGGTTGTTATCTCTGCCCCAAGCAAAGACGCACCCATGTTTGTTGTTGGTGTCAATGAGGACAAGTACACCTCGGATGTTAACATTG

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G176307_T01 (Zea mays), 3'ss of exon 5
ctctttttctgtattggtttgatttatagcttctttgtgatgattgtttagttcattttaatggtctatgtgggctgatttgggattttttggtga----gcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG
 | |  |  | ||    || |  ||||    | |    | |   |   |   |  |  || || | |    |     | |  || |||  || ||      ||||||||||| ||||||||  |||||||||| || ||||| ||||| |||||||||||  | |||||||| |||||||| |||||| | || ||  ||||||
gtataatcatctacctatt-gtgttattctatttccagggtatataccttactagtcctagtgttatggaagaatctaat--ggttttcctgttgcttttacagGGTGGTGCCAAGAAGGTTGTCATCTCTGCTCCTAGCAAGGATGCCCCCATGTTTGTCGTTGGTGTCAACGAGAAGGAGTACAAGTCTGACATTAACATTG

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G071630_T02 (Zea mays), 3'ss of exon 4
ctctttttctgtattggtttgatttatagcttctttgtg-atgattgtttagttc--attttaatggtctatgtgggctgatttgggattttttggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG
          ||||   |||| |||||   | |   ||  ||   |  |||||||     ||    |  | |   |  |    ||    ||||       ||||||||||| ||||||||  |||| ||||| || ||||| ||||| |||||||| ||| | |||||||| |||||||| |||||| | || ||| ||||||
----------gtataattttgttttat---tccagggtatataccttattagttccagcattggaagcatctaacgattttcctgttgctttt------acagGGTGGTGCCAAGAAGGTTGTCATTTCTGCTCCTAGCAAGGATGCCCCCATGTTCGTTGTTGGTGTCAACGAGAAGGAGTACAAGTCTGACATCAACATTG

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|33406621|gb|CF212248.1|CF212248
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161706852|gb|FC055537.1|FC055537
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161720959|gb|FC070345.1|FC070345
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|110703819|gb|EE080998.1|EE080998
EST:     CTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: CTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|110701389|gb|EE078905.1|EE078905
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161710748|gb|FC060307.1|FC060307
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|110697161|gb|EE073909.1|EE073909
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161721814|gb|FC070505.1|FC070505
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161716699|gb|FC065571.1|FC065571
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161708621|gb|FC058356.1|FC058356
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAAGTAATCATCTCTGCCCC
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCC
EST: gi|30134770|gb|CB920108.1|CB920108
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCTACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|110687944|gb|EE065928.1|EE065928
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|110373445|gb|EC937683.1|EC937683
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161713863|gb|FC062559.1|FC062559
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|110707375|gb|EE083731.1|EE083731
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161718038|gb|FC067580.1|FC067580
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|71857565|gb|DT006620.1|DT006620
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161712390|gb|FC061695.1|FC061695
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161715330|gb|FC065818.1|FC065818
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|110688396|gb|EE066900.1|EE066900
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161719339|gb|FC068279.1|FC068279
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161720005|gb|FC067735.1|FC067735
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATG
EST: gi|161708879|gb|FC060092.1|FC060092
EST:     AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAG                         GGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTC
genomic: AATCTACTGGAGTGTTCACTGACAAGGACAAGGCCGCTGCCCACTTGAAGgtctggtttc ... tggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttagttcattttaatggtctatgtgggctgatttgggattttttggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG
                                        tttttt  CT-rich tract
      ttcattttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctttttctgtattggtttgatttatagcttctttgtgatgattgtttagttcattttaatggtctatgtgggctgatttgggattttttggtgagcagGGTGGTGCAAAGAAGGTAATCATCTCTGCCCCCAGCAAAGATGCTCCCATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggctga