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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA

Basic information

species Vitis vinifera
transcript Vv19s0015g01730.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatcc--ttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
                                       ||||  | | | ||| |   ||||   ||  || | || |   ||     |  |     |  ||| |  ||||  |     || || |||   ||  | ||||||||||| ||||| ||||| |||||||| ||||| || || ||||| ||||||||||| ||||| || || || || || || || ||| |||| || |
gttacatggtcacatacctttttactcactagagctgtttttatttaacatgtttaca-aatc---ttagttgttaggtcagatctccttgatgattcttttttgaaattaaccacttaattctacttatgttt--tacagTACTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGCGATAATGATGTTGCAA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 7
------------------------------------------------tttaacttagaggttaatgcaat-cagattgcttttcagtttttatgcatgttgt--atacttc--ctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
                                                ||||  | | | ||| |   |||     ||| |  |   |   ||   |  |  |  ||  |||   ||| |  ||||  ||    |  | |    ||  | ||||| ||||| ||||| ||||| |||||||| ||||| || || ||||| ||||||||||| ||||| || || || || || ||||| ||| |||| || |
gtaacatggtcacatctattactgtttttgtttttcactagttctgtttttatttaacatgtttacaaaatattagttgttacttgttaggtacagacttccttgatgattcatttttgaaattaaccatttaatgctattccttttttacagTATTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGATAATGATGTTGCGA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------tttaacttagaggttaatgcaatcagattgcttttcagtttttatgca---tgttgtatacttcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
                                                                               || | || | |   || |    ||   |||| |        ||| ||    |||||| ||||   | | ||  |  |    ||  ||    |  ||    ||||||||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||| ||||| || || || || || ||||||||| |||| || |
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------tttaacttagaggttaatgcaatcagattgctt---ttcagtttttatgcatgttgtatact-tcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
                                                                          |||| || | |   || |    ||   |||| |   ||  |||    |   |||| | |||| |  |||  ||||  |         || |  | ||    |||| |||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||| ||| | || || || || |||||||||||| |||| || |
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttc-cacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 7
tttaacttagaggttaatgcaatcagattgcttttcagttttt-atgcatgttgtatacttcct------ttaatgttaataatccttttatttaat-cttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
   || ||  |   | | || ||||  ||  || |||| |||| |||  |  | | |||    |      ||  ||||  | || |||  || |||| |||  ||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| |||||||||||||| |||||||| ||||
---aattttaa---tcaagctatcattttctttatcagattttgatggttaatatctaccatttaatggatttgtgttgctgattctt--atgtaatacttgttgcagTATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
tttaacttagaggttaatgcaatcagattgcttttcagttttt-atgcatgttg-tatacttcctttaatgttaataatc--cttttatttaat-cttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA-
       ||    | || || |||| |||  || ||||  ||| |||    | | ||   |||  |  || ||  |       | |||| |||| |||  ||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| |||||||||||||| |||||||| |||| 
-----aatattaatcaa-gctatcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 5
tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatccttttatttaat-----cttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
  |||| ||    |   |    | |  |        | |  | || |   || | |  || |  || | ||| |||   |||  | ||||     |||  ||||||| || |||||||||||||||||||||||||||||||| ||||| || |||||||| || ||||||||||| |||||||||||||| |||||||| || |
--taacatatt--tcgttttttttatgtctaccaatattagtaattccctttttttgtttaccgta-tattagtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTACGCTGATATCATTATACCCCGTGGAGGAGATAATCATGTGGCTA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
-tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatcctt-ttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
  |    |   ||||||     || | ||     |    | ||  |   | |||  |||    | | | || | |  | ||| | || ||  |||  ||||||| || |||||||||||||| ||||||||||||||||| ||||| || ||||||||||| ||||||||||| ||||||||| |||| |||||||| || |
gatcttttcgtaggttatgattat-aaatcaagctaatatattccttttttttgcttaccatatatta-gtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------------------------------------------------tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcc---ttta-atgttaataatcct--tttatttaat--------cttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
                                                                        ||||| |   |  ||  |   ||| |  || ||||   || | ||    |||      || |   | || |||||  ||  | |  ||||| | ||         ||  ||||||||||||| ||||||||||| |||||||||||||| || |||||||| ||||| ||||||||||| || || || ||||| || || ||||||||||| |
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgttttt---ttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
                      |  |  ||  | |   || || |   |     ||| || ||||| |  |  |  | | | | |  ||   |  ||||||||||||| |||||||||||||| ||||| || || ||||| ||||||||||| || |||||||| || |||||||| || || || || ||||| || |
--------------------gttttgtgtggctgtatattcttgtt--ttgcaaataatttctttatttatgtt--ttcatgtgtgaaactcttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 6
------tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
         | | | |  ||  |||   ||  | |||      |      |  || | |||   |      ||||   || | |    |  |  |  |    ||||||| |||| |||||||||||||| |||||||| |||||  | ||||||||||||||||| ||| ||||  | ||||||||||||||||||||||| || |
gaccatcccagccttgttgtccatggcgtcttagtgc------gaacacttcgatctcgtagcttatacggaatgaagatgaactaacttctggaggtgtacgcagTACGCAAAGTTTGTGAAGCCAGCGTTTGATGATTTTATTTTGCCAACAAAGAAGTATGCGGATGTCATCTTACCCCGTGGAGGAGACAATCATGTGGCTA

upper sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S488_8V6.1 (Physcomitrella patens), 3'ss of exon 6
tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatcc--ttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
    |  |  |   ||       |||  |  |    | ||||    ||||| |  |   ||   || ||   | || |   || |||||    || ||||||||  |||| |||||||||||||| |||||||| |||||  | ||||||||||||||||| ||| ||||  | |||||||| |||||||||||||| || |
-gccatctgaatcctatccgtggcagcgtaatgagtacttttggatcatgtagcgt-tgtcgcatattgaagagaaacgaattgtattttggatttgtgcagTATGCAAAGTTTGTGAAGCCAGCATTTGATGATTTTATTTTGCCAACAAAGAAGTATGCGGATGTCATCTTACCCCGTGGTGGAGACAATCATGTGGCAA

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|161718287|gb|FC066969.1|FC066969
EST:     GGCGTGATACAGTTGAGAAGGGTAGAGATATTGGTATGGTACTTGATCAG                         TACTCGAAATTTGTGAAGCCAGCTTTTGATGACTT-ATAC
genomic: GGCGTGATACAGTTGAGAAGGGTAGAGATATTGGTATGGTACTTGATCAGgttagtaact ... cttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgttgtatacttcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
                 tttaatgttaataatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - gcaatca
- - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tacttcc