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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttggaactttgttcacctcccaaaccttggggaatattgtaaccttccataattgggtcttgaatttgctttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG

Basic information

species Vitis vinifera
transcript Vv12s0059g01930.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 6
-----gttagtttggaactttgttcacctcccaaaccttggggaatat----tgtaaccttcc--ataattgggtcttgaatttgctttccttgt----------agGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG
       || |   |   | |  |||| |||   | |||     |||     ||| ||||| |  | | ||   | || || |    |  | | |          ||||   |  || ||| | |||||||| ||||||||| |||| || || || || ||||||||||| |||||||| |||||||||  ||| |||||
gtacaactaatcgtgttttattgtcacatcctccatcttcttccatagcacatgttaccttactgacacttcaattttaaactaatatgacctatctacttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGTGCCCGGGGCTTATGTGTTATGGTATCGGCCTCTTTATAATGCAATGAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 6
---------------gttagtttggaactttgttca-cctcccaaaccttggggaatattg-taaccttccataattgggt---cttgaatttgctttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG
               |      ||  |  |  || | | |||   | |          ||  | ||  | ||   |          |||  |  ||        ||||   |  || ||| | |||||||| ||||||||| |||| || |  || || ||||||||||| |||||||| |||||||||  ||| |||||
gtataactaaagtgtgccttactgtcatctcatttatcttcctccatcacactttgccttactgacgcttcaagttcaaactaatatgacctatctacttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTGGGGCTTATGTGTTATGGTATCGACCTCTTTATAATGCAATGAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 7
gttagtttggaactttgttcacctcccaaaccttggggaatattgtaaccttccataattgggtcttgaatttgctttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG
  ||   || | | || |     |        ||     | ||| || | | |    | |     ||| ||   |  |  |   |||    |  || |||||  | || || ||||||||| |||| || ||||| || || ||||| ||||||||||||||||| |||  ||| |||||
-gtatactgaatcattttggtgttatttgttgttctatca-attatatcgtgctcacactttaaattgtatcaaccgttttc--agGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 7
gttagtttggaactttgttcacctcccaaaccttggggaat--attgtaaccttccataattgggtcttgaatttg-ctttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG
             |||||    |  |   |  |||  | ||  ||| |       |||  ||   |     | ||| |||||| ||||||||| || || ||||||||||| || ||||| ||  | || || | ||||||| | ||||||||||||||||| |||||||||||||| |||||
------------gtttgtcttgcaactggatattgatgcatcaattttgttaagtcatgcttaatttaccgacttgtctttccatgtagGTCCAACCATCTGGTTTCTTGCTATTATCTATTTTATTTCTGGTGCTCCAGGATCCTATGTGTTGTGGTATCGCCCTCTTTATCGTGCTATGAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 7
gttagtttggaactttgttcacctcccaaaccttgggg-aatattgtaaccttccataattgggtcttgaatttg-ctttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG
             |||||    |  |   |  |||    ||| |||| |  |  |||  ||   |     | ||| || ||| ||||||||| || || ||||||||||| || ||||| ||  | || || | ||||||| | ||||||||||||||||| |||||||||||||| |||||
------------gtttgtcttgcaactggatattgcatcaatcttgttaagt--catgcttaattaacagacttgtctctccatgtaggtccaaccatctggtttcttgcaattatctattttatttctggtgctccagGATCCTATGTGTTGTGGTATCGCCCTCTTTATCGTGCTATGAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G37590.1 (Glycine max), 3'ss of exon 5
gttagtttggaactttgttcacctcccaaaccttggggaatattgtaaccttccataattgggt-cttgaatttg-ctttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG
             ||||||   || | | |  |||    |      |   |       |||  | | | |||||| ||| |||||||||||   |||| ||||||||  | ||||| |||||  | || || ||||||| | | |||||| ||||||||||||||||||||||||| |  ||
------------gtttgttttactactagatattgaaccaacaaacacagtagggctgttgtttacataaatttgtcttaccttgtagGTCTTTCAATCTGGTTTCTATCTATCATATACTTTATTTCCGGTGTTCCAGCATCCTATGTGATGTGGTATCGTCCTCTTTATCGTGCGACAAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagt-ttggaactttgttcacctcccaaaccttggggaatattgtaaccttccataattgggtcttgaatttgctttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG
|| ||| |||||||  |    |  | ||||   | |    |   ||||   | |  ||||  | |     || |  |||   ||||||||| ||||| |||||||| || || ||||| ||| ||||||||||||| ||||| |||||  |||||||||| ||||||||||||||||||||
gtaagtcttggaacagttaaaatttaccaag--tagactgaacctgtatgatgc--taatctgctgacttatgtattttggctgtagGTCCAACAATATGGTTTCTAGCTATTATCTATTTCATATCAGGGGTTCCTGGAGCGTATGTTATGTGGTATCGCCCTCTTTATCGTGCCATGAG

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:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|77584192|gb|DV221151.1|DV221151
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|27584710|gb|CB007405.1|CB007405
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|349811810|gb|FQ410607.1|FQ410607
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGCGTTCCCG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|27586086|gb|CB008781.1|CB008781
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTCAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|110385536|gb|EC950069.1|EC950069
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|110388736|gb|EC953515.1|EC953515
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|27584919|gb|CB007614.1|CB007614
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|110376126|gb|EC941168.1|EC941168
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|110357026|gb|EC920280.1|EC920280
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|32245954|gb|CD711773.1|CD711773
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|71870414|gb|DT019469.1|DT019469
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|110699817|gb|EE077160.1|EE077160
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|71870410|gb|DT019465.1|DT019465
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG
EST: gi|110722937|gb|EE099679.1|EE099679
EST:     CTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGGTTC-
genomic: CTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGG-AAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGG-TTCC
EST: gi|110722049|gb|EE097937.1|EE097937
EST:     CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAG                         GTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAAGGGTTCCAA
genomic: CCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttgg ... ttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggggaatattgtaaccttccataattgggtcttgaatttgctttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG
           ttgtaac  putative branch site (score: 2)
                                       tttgctttccttgt  putative PPT
       aatattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttggaactttgttcacctcccaaaccttggggaatattgtaaccttccataattgggtcttgaatttgctttccttgtagGTCCGACAATTTGGTTTCTTGCCATCATCTACTTCTTATCAGGGGTTCCAGGAGCTTATGTGTTGTGGTATCGTCCTCTTTATCGTGCCATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT