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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatttgatttctaatgatgccaaaatcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG

Basic information

species Vitis vinifera
transcript Vv08s0007g07960.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 3'ss of exon 2
gtgcatttgatttctaatgatgccaaaatcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgt-agGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG
                        |  ||| | ||  | |   ||   || || || |    | |   ||||   |  |||   | ||   | |||| ||||||||||||| ||||||||||| || || ||||||||||| |||||||| ||||| |||||||||||| | |||||| |||||||   || ||||||||
----------------------gtaggatcttgtttccaa---attttttccatggattaagtgccatttgtc-tcaattgagctgttatgtgatgtcagGAAGCCAAGGAGAAATTTCAGCAGCTTCAGAAGGTGATATCTATTCTTGGGGATGAGGAGAAAAGGGCATTATATGATGAGACTGGAATTGCTGATGATG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 2
gt-gcatttgatttctaatgatgccaaaatcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG
|| | || | |    |||  |||    |||  | |||| ||   ||    ||||| |    | |      | | |   | | | ||  |         |||||||||| || || |||||||| || || ||||| ||||| |||||||| |||| ||||||||| ||  | |||||| |||||||      ||||||||
gtagtatctcaaccataaacatg----aatgtttttctacaggcatttagtgcaaag----tatctcaaatataatgttatatgttgct---------agGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G32480.1 (Glycine max), 3'ss of exon 2
---gtgcatttgatttctaatgatgccaaaatcctattctccatata-tccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG
        | |   | || |  ||||||  ||  | || ||  || | |   ||  | | || |     || |  ||    || |||| ||    |  || ||||||| ||||| ||||| |||||||| ||||| |||||||| ||||| || |||||||||||  | || |||||||||||||||||||||||||||||||
caaccttttatatctcctgaatatgccatcatggtcttttcactagaatatattttaggtgttgacacttg-taattga--ttagtttcttgtgttgttgcagGAAGCTAAGGAGAAATTCCAGCAACTGCAAAAAGTGATATCGATTCTCGGGGATGAAGAGAAGCGAGCTCTCTATGATCAGACTGGTTGTGTTGATGATG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 2
gtgcatttgatttctaatgatgccaaa-atcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG
     |||  | |||| || | ||     |||| |  |  || |||       |  | ||  |||  |||||| |    |  | |||| |        ||||||| || | ||| ||||||||| | ||||| || ||  | |||||||| |||||||| ||| ||||  | ||||||||||||||||||||||||||||
----gttttttgtctagtgtttcctgttgtcctctaattgatttattaaagttatagatg--tttgcggttgtaattgatcatcttttac--------agGAAGCTAAAGCAAAGTTTCAGCAATTGCAAAACGTTATCGCTATTCTTGGGGATGAAGAAAAACGGGCTGTTTATGATCAGACTGGTTGTGTTGATGATG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 2
gtgcatttgatttctaatgatgccaaaatcctattctcca-tatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG
  |  |||  | |||| || | ||    |  | | ||| | |  ||   ||| ||   | | | | | |  |||    ||  |  | ||      |  ||||||| || | ||| ||||||||| | ||||| || ||  | |||||||| |||||||| ||| ||||  | |||||||||||||||| |||||||||||
--gtgttt--tgtctagtgtttcc----tgttgtcctctaattgatttattgaaattatagatgt-tagcggttgtaattgatcatcttt-----tacagGAAGCTAAAGCAAAGTTTCAGCAATTGCAAAACGTTATTGCTATTCTTGGGGATGAAGAAAAACGGGCCGTTTATGATCAGACTGGTTTTGTTGATGATG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgcatttgatttctaatgatgccaaaatcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG
                 | |   || | || | | ||  | ||||   |||   |  |  ||| |  |  | |  |   | || ||||      |  ||||||| || || || || ||||| || ||||| |||||||||||||||||||||||||||||||||||| |||||||||| ||||| |   |||||||||
---------------gttaaatacacactcttttacttgagatattttttg---gattcatttacatgaagat-tctactattgttttgt----tacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgcatttgatttctaatgatgccaaaa----tcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG
||  |  |||    |  || |  |   |    || || | |  |    ||  ||   |   |    || |    |  |  |||  |||| ||  |  ||  |||| || || || |||||||||||  | |||||||| || || ||||| ||||||||||||||||| ||| |||||||||| ||||| |  ||||||||||
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattc--aattttacattgtaaccggaattcttgtttttcttatccaatacagGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG

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|351015510|gb|FQ447339.1|FQ447339
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
EST: gi|349825564|gb|FQ419481.1|FQ419481
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
EST: gi|352794289|gb|FQ479531.1|FQ479531
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
EST: gi|351028672|gb|FQ446345.1|FQ446345
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
EST: gi|351054628|gb|FQ456825.1|FQ456825
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCCTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
EST: gi|110686833|gb|EE063714.1|EE063714
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
EST: gi|349827514|gb|FQ422382.1|FQ422382
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
EST: gi|351048863|gb|FQ431528.1|FQ431528
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
EST: gi|351023284|gb|FQ432667.1|FQ432667
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
EST: gi|351040488|gb|FQ434621.1|FQ434621
EST:     ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG                         GAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT
genomic: ACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAGgtgcatttga ... cctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG
                        ttgttaccctttgttt  CT-rich tract
                                 tttgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatttgatttctaatgatgccaaaatcctattctccatatatccgttgcaagggtggttttctggttgttaccctttgtttttttccctcatgtagGAAGCCAAGGAAAAATTTCAGCAACTACAAAAGGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCACTCTATGATCAGACTGGTTGTGTTGATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA