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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatcggatgtccatcccttgcaagttcctctgttatttctttgaaatctgttttgccccattccatgtaatactctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA

Basic information

species Vitis vinifera
transcript Vv14s0030g00750.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 5
--gtcatcggatgtccatcccttgcaa---gttcctctgttatttctttgaaatc-tgttttgccccattccatgtaatactctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGAT--GCAACTGCACTTTCTGAATCA
     |  | || | |    ||  |||    || ||  | |  ||  ||||  |  |   |||    |||| | |||      | || |   || | ||   |||   | |  ||    |||| |    | |||    ||||||||||| |||   | ||||| || |||||||| ||||||||||| || || |||||||||||||| ||||| ||||  |||  | | |   | | ||  
gtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattgggatattctacgtaccctcttgttcttatatagcttttcttcatcaaaaattg---ctggttcatgtctgagtgtagGAGGAAGATATGCTCCTAGAGAACGTCTACTACTCAGAGATGAAAGACGCTGGGTTCTTTGATGCTGACTGGGATTGATCTGCAGATAC-CACGCCGTATG-

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G37380.1 (Glycine max), 3'ss of exon 5
gtcatcggatgtccatccct---tgcaagttcctctgttatttct--ttgaaatctgtt-ttgccccattccatgtaatactctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA
|||||   ||| || || ||   |||  |    || ||| || ||  |  ||   |||| |||         | |  |  ||   || | | ||||||  || | | | ||| ||||         ||   |||| |||||||||||||||||||||||||||||| ||||||||||| |||||||||||||| |||||||| || |||||| | |||||      |   | ||  || |
gtcat--aatgcccttcacttaatgcctggggttcagtttttactagtcaaaccatgttattgtttgtagttaggacagtcttccttctttcattgatctgactagttgtag-ttat---------tgtgatgattacagGAGGAAGATTTGCATTTGGAGAATGTGTACTACTCTGAAATGAAAGATGCCGGTTTCTTTGAAGCAGATTGGAACTGATGTGGTATCGACTGCTAGATTA

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G30010.3 (Glycine max), 3'ss of exon 3
gtcatcggatgtccatcccttgc------aagttcctctgttatttctttgaaatctgttttgccc-cattccatgtaatactctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA
|||||   ||| || || |||          ||||   | |||||  |      |  || |||     | |      ||| |||  | || | ||||||  || |   |    ||| | | | | ||       || | |||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| || |||||| | |||||      |   | ||  || |
gtcat--aatggccttcacttaattcctggggttcagtttttattagtcaagccttggtattgtttgtagtttggacaatcctccttctt-tcattgatctgactaatt----gttgttatttgatg-------attatagGAGGAAGATTTGCATTTGGAGAATGTGTACTACTCTGAAATGAAAGATGCTGGTTTCTTTGAAGCAGATTGGAACTGATGTGGTATCGACTGCTAGATTA

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G40260.2 (Glycine max), 3'ss of exon 4
gtcatcggatgtccatcccttgcaagttcctctgttatttctttgaaatctgttttgccccattccatgtaatactctattttatgattgattagattcgctatag-gttatgactgg-gtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA
                                                |   | | |    |||   || | |  | || ||  | |  ||  |  |||  |  |  | | |||||   || |  | | ||  ||||||||| |||| |||||||| ||||| || || || |||||||||||||| || ||||||||  | || |||||||||||      ||  |    | | |
-----------------------------------------------gttaatgtcgttt-attttttgaacttttataattgtttagagacaactttccatgcactggtctgactactgttttttttcatttcagGAGGAAAATTTCCATTTGGAAAATGTGTATTATTCCGAGATGAAAGATGCAGGTTTCTTTGACACGGACTGGGAGTGATGATGTATCAGCTATAAATTGA

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G42870.2 (Glycine max), 3'ss of exon 4
gtcatcggatgtccatcccttgcaagttcctctgttatttctttgaaatctgttttgccccattccatgtaatactctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA
                                          || |  ||  ||||      ||  |  |  || | |  ||||      |||  |    ||    |   |||||     |  ||| ||  ||||||||| |||| |||||||| ||||| || || ||||||||||||||||| || ||||| ||  | || |||||||||||      ||  |  | |||  
-----------------------------------------gttaatgtcgtttttttt---tttaactttttattattgtttaaagacaattccacgtact----ggcctgactattgtttttgt-atttcagGAGGAAAATTTCCATTTGGAAAATGTGTATTATTCTGAGATGAAAGATGCGGGTTTCTTCGACACGGACTGGGAGTGATGATGTATCAGCTATTAAATTG

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G05010.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcatcggatgtccatcccttgcaagttcctctgttatttctttgaaatctgttttgccccattccatgtaatactctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA
                            ||   |  ||  || | |     ||     | |  |     || |||  |  || || |     |   || |   ||   |     || || ||||       |||||||||||| || ||||||||||||| ||||| || || ||||||||||| || ||||| || ||||||||||| | |    | | |   |      |||
---------------------------accatcgccatcactattaccatagtaccatcaccattaccatagtaccat-cttcatcaccacatgatttggtgctaaaattcacttgtgtttgctt------cagGAGGAAGATCTGAATTTGGAGAATGTCTACTATTCAGAAATGAAAGATGCTGGATTCTTCGACGCTGATTGGGAATAACAGGAGTCCTAGTGTCTTGTCA

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G27210.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcatcggatgtccatcccttgcaagttcctctgttatttctttgaaatctgttttgccccattccatgtaat--actctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA
                                                             | ||    | ||  |   | | | |       |   | || || ||   |   | ||||| |||||      ||||| ||||||||| | |||||||||||||||||||| |||||||| ||||| || || || ||  |||||||||| |    | |  | |         |  
-----------------------------------------------------------gtaatcatcatcattcatcttctctcactgactctctcactctctctaaaatgcaaatgggtttgctg------cagGAAGAAGATTTGAACTTGGAGAATGTATACTACTCAGAGATGAAGGATGCTGGATTTTTCGACTCTGATTGGGAATAGGACTAGGGTAACAAACATCTTC

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|30131882|gb|CB917221.1|CB917221
EST:     CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAG                         GAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
genomic: CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAGgtcatcggat ... gtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
EST: gi|22012612|gb|BQ797646.1|BQ797646
EST:     CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAG                         GAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
genomic: CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAGgtcatcggat ... gtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
EST: gi|110365218|gb|EC927851.1|EC927851
EST:     CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAG                         GAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
genomic: CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAGgtcatcggat ... gtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
EST: gi|30133320|gb|CB918659.1|CB918659
EST:     CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAG                         GAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
genomic: CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAGgtcatcggat ... gtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
EST: gi|110389708|gb|EC954568.1|EC954568
EST:     GCAGACTTTTTCCAG                         GAGGAAGATTTCCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
genomic: GCAGACTTTTTCCAGgtcatcggat ... gtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
EST: gi|110703012|gb|EE079484.1|EE079484
EST:     CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAG                         GAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
genomic: CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAGgtcatcggat ... gtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
EST: gi|110414461|gb|EC980293.1|EC980293
EST:     CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAG                         GAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
genomic: CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAGgtcatcggat ... gtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
EST: gi|110394639|gb|EC959842.1|EC959842
EST:     CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGATTTTTTCCAG                         GAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC
genomic: CCTTTTATCTTCCCCTTCTATATATTACATTTCTAGCAGACTTTTTCCAGgtcatcggat ... gtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA
      gattgat  putative branch site (score: 4)
       attgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatcggatgtccatcccttgcaagttcctctgttatttctttgaaatctgttttgccccattccatgtaatactctattttatgattgattagattcgctataggttatgactgggtgtgctgtgatgacagGAGGAAGATTTGCATTTGGAGAATGTATACTACTCTGAGATGAAAGATGCCGGCTTCTTTGATGCTGATTGGGAGTGATGCAACTGCACTTTCTGAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT