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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaaccttaaagtcctgtttgatagaagttcaagtttcaaatgtcccaaagtgattttctcttgtggaatccatagatgcatttctcttctcttt...

Basic information

species Vitis vinifera
transcript Vv12s0059g01930.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 5'ss of exon 5
AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaaccttaaagtcctg---tttgatagaagttcaagtttcaaatgtccc-aaagtgattttctcttgtggaatccatagatgcatttctcttctcttt
|| |||||||| || |||||  ||||||||||||||||| ||||||| ||||||||||| | ||| | | |||| ||| |||||||  |  |||  ||||||| |||    ||  |||  |    ||| |      ||    |  |  ||||    ||||   |         |  ||| | | |  | |   |  ||||    
AACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATACCTTGCATTTTCTTCATTGTTGGgtaagtgttagttttagttttaagttttaactctctttttgttccctcatgttgggaaagctgtcacaagaactaaaatacctggtggaaccacaattct----

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G100809_T01 (Zea mays), 5'ss of exon 5
AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatg----tgaaccttaaagtcctgtttgatagaagttcaagtttcaaatgtcccaaagtgattttctcttg-tggaatccatag-atgcatttctcttctcttt
|||||||| || ||||||||||| || || ||||||||| | ||||| ||||| ||||||| ||| | | |||| ||| |||||||| || ||| |||||||| |    | |   |  ||    |||| | ||| | | |   | |  | ||||     || | | |||||   |  | |  || | ||  || | | || | || 
AATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATACCTTGCATTCTCGTCATTTTTGGgtaagcttttaagtgtccaaaatgtgttggttagtactac---tgtacagtgtctt---gtcactctctctgacttaagtatattgtattgatcttttttttatta

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 5
AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatg----tgaaccttaaagtcctgtttgatagaagttcaagtttcaaatgtcccaaagtgattttctcttgtggaatccatagatgcatttctcttctcttt-
|| ||||| || ||||||||||| || || || |||||| | ||||||||||| ||||||| ||| | | |||||||| |||||||| |  |||  ||||||  |    | |   || ||    |||| | ||| |  | |   | | | | ||      |   | |||||     || | |||  || |||  |||| | ||  
AACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagcttttaagtgttcaaaatgtgttggttagta--ttattgtactagtatct-ggtctctctctctctgactcaagc-atat-tgtattgatctttttttat

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA12G11820.2 (Glycine max), 5'ss of exon 6
AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgt-gaaccttaaagtcctgtttgatagaagttcaagtttcaaatgtc--ccaaagtgatttt--ctcttgtggaatccatagatgcatttctcttctcttt
||||||||||| ||||| ||| | |||||||||||||||||||| ||||||||||| ||||  || | | | |||||| ||||||| || ||||  |||||||||| ||||   | |    | ||  | |    || ||||   || |  |  | ||  ||||      |  | || | |   ||| ||  ||  |         
AATTGGCCACCTTTTTTTCCCATCATTCATCATGACATTGCAAAGGAAATACCAATACATCTTCAAAGGATCCAGTACATTGCATTTACAACATGGTTGGgtatgttgaactccagaactgtcttctagaatgttttaagtcataactagctactaacttgatgagaagtaatctgtactttgtagttgagttggtaaat-----

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA06G45160.1 (Glycine max), 5'ss of exon 6
AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgt-gaaccttaaagtcctgtttgatagaagttcaagtttcaaatgt---cccaaagtgattttctcttgtggaatccatagatgcatttctcttctcttt
||||||||||| ||||||||| | |||||||||||||||||||| ||||||||| | ||||  || | | | |||||| ||||||| || ||||  |||||||||| ||||   | |    | ||  | |    || ||||   || |     | | | | ||  |  | ||    ||  | ||  |   ||| |||| |    
AATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTACATTGCATTTACAACATGGTTGGgtatgttgaactccagaactgtcttctagaatgtttgaagtcataactagctactcgatgagaagtaatattaacaaaatc-taacttggtttttcttatg---

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA13G37590.1 (Glycine max), 5'ss of exon 4
AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaaccttaaagtcctgtttgatagaagttcaagtttcaaatgtcccaaagtgattttctcttgtggaatccatagatg--catttctcttctcttt
||||||||||| |||| |||| | |||||||| |||||||||||||||||||| || ||||  ||     | ||||| |||||||| || ||||  || |||||||  |  |  |  |  | |||| || |  || | |||| |    |  | |  || ||||||       | |  |||||     |  ||| || |  ||
AATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTATGTTGCATTTACAACATGGTTAGgtatgttgaagtctagattttttttgttatagatt-atgttttagtcataactacttg-ttttctgagacttagttaatagaaaattacatctgttttgctt

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA12G32860.1 (Glycine max), 5'ss of exon 4
AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgt-gaaccttaaagtcctgtttgatagaagttcaagtttcaaatgtcccaaagtgattttctcttgtggaatccatagatgcatttctcttctcttt---
||||||||||| |||| |||| | |||||||| |||||||||||||||||||| || ||||  ||     | ||||| || ||||| || ||||  || ||||||| |||   || |    | |||  |    | | | ||||      |    || |  |||| | || | || |  ||   |     |   ||   ||    
AATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTATGTAGCATTTACAACATGGTTAGgtatgttgaagtctagaaattttttttgttatggattatgttttggtcat----aactacttttttgttatagattatatctgttttgcttcatttgattagta

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 5'ss of exon 5
AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaaccttaaagtcctgtttgatagaagttcaagtttcaaatgtcccaaagtgattttctcttgtggaatccatagatgcatttctcttctcttt-----
|| |||||||| ||||| || || || |||||||||||| ||||||| ||||| |||||||  ||||   | || || ||||| |||||  ||    ||||||||||     |    |      ||||  | |    |  | ||  ||   || ||     || |||||    ||   || |     ||    ||| |||     
AACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATATGTTGCTTTCACATCAATGCTGGgtatgtgttttctc---tttcaaatgatcaacgc---atctgcagttgcaacagaggtggatt-tcttgatatattagtaaacaatcttaatctctgtttggtag

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|110418607|gb|EC984768.1|EC984768
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|77584192|gb|DV221151.1|DV221151
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|27584710|gb|CB007405.1|CB007405
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|349811810|gb|FQ410607.1|FQ410607
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|27586086|gb|CB008781.1|CB008781
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|110385536|gb|EC950069.1|EC950069
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|110388736|gb|EC953515.1|EC953515
EST:     AGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: AGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|27584919|gb|CB007614.1|CB007614
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|110376126|gb|EC941168.1|EC941168
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|110357026|gb|EC920280.1|EC920280
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|32245954|gb|CD711773.1|CD711773
EST:     CCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: CCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|71870414|gb|DT019469.1|DT019469
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|110699817|gb|EE077160.1|EE077160
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACAACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|71870410|gb|DT019465.1|DT019465
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|110722937|gb|EE099679.1|EE099679
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACAACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
EST: gi|110722049|gb|EE097937.1|EE097937
EST:     ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACAACATATTTGG                         GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA
genomic: ACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaac ... tgtcatgcagGTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTACGTTGCATTCACGACATATTTGGgtatgtgaaccttaaagtcctgtttgatagaagttcaagtttcaaatgtcccaaagtgattttctcttgtggaatccatagatgcatttctcttctcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatagaa