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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgagattctcccacaatctaatcattaacaggtagctttagtgtcgcatgtttaatttccttgaatattttgcttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG

Basic information

species Vitis vinifera
transcript Vv00s0349g00020.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g06120.3 (Oryza sativa), 3'ss of exon 6
tttgagattctcccacaatctaatcattaac---aggtagctttagtgtcgcatgtttaatttccttgaatattttgcttcttattatccc-tttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG
       || ||  | |   | | |||  ||   | | ||| || || |  | |       ||   ||    ||     |||  ||||    |  |  ||||||||||| |   ||||||||||||| |||||| |||||||||| |||||||| ||||| ||||||||||| ||||| ||||| ||||| | |||||
----gttttatctgaaagaattaccatgcacactatggagcgttcgtatatcctaagagccttttatgttacttaaaactctgtttatgttatgccgctgacagGGAGGTTGCATTGATGATTTCCTATCACATTTGATGTGTTGTTGCTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG

upper sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G027821_T01 (Zea mays), 3'ss of exon 6
tttgagattct-cccacaatctaatcattaacaggtagctttagtgtc--gcatgtttaattt--ccttgaatattttgc-ttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG
      ||| |   ||      | ||   || ||    ||||||   |  |||   ||| |    |||| | ||  |    |||| ||  ||    |  |  |||||||||||  | ||| || ||||| ||||||||| ||||||| ||||| || ||||| ||||||||||| ||||| ||||| || || | |||| 
------attgtgtacattggtgactcgacaatagccttctttagatactagcaaacttattgaagccttcagtacctgaagttctgatggtcgtgcttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA

upper sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G08430.2 (Glycine max), 3'ss of exon 5
tttgagattctcccacaatctaatcattaacagg----tagctttagtgtcgcatgt-ttaatttccttgaatattttgcttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG
     |  | |   | ||| ||| |||  |  ||    |||  |||      ||| |  |  | || || ||| ||||  | |  |      |||||| ||  |||| |||||  |||||||||||||||| ||| ||||||||||||||||||||||||| ||||||||| |||||||||||||||||||| ||  ||
-----gtatttgttaaaatttaagcatacatcggaatttagtattaagcatacatttgctggtctctttaaatgtttttttacccacagctactttctatgctagGGGGGCTTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCCCTTGTGCAAGAATGGAGAGAAGTGGAGATCCGTGGGCTTACTG

upper sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G36860.1 (Glycine max), 3'ss of exon 7
tttgagattctcccacaatctaatcattaacagg----tagctttagtgtcgcatgtt--taatttccttgaatattttgcttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG
     |  | | | |  || | | ||   |  ||    |||  |||      ||| ||     | || || ||| |||| |   |   ||   |||||| || ||||| || ||  |||||||||||||||| ||| ||||||||||||||||||||||||| ||||||||| |||||||||||||||||||| ||  ||
---atgtatttgctaggatttgagcacacatcggaatttagtattaagcatacattttgcgggtctctttaaatgttttacccatagcta---ctttctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCCCTTGTGCAAGAATGGAGAGAAGTGGAGATCCGTGGGCTTAGTG

upper sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G05130.1 (Glycine max), 3'ss of exon 7
----tttgagattctcccacaatctaatcattaacaggtagctttagtgtcgcatgtttaatttccttgaatattttgcttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG
    || |||          ||| ||   | | | | | ||  ||  | | | || ||    |  |||  || ||||  |    |||    | |||| || ||||| || ||  |||||||||| || || ||| ||||||||||||||||||||||||| |||||| |||||||||||||||||| ||||||| | |
aaggttggagtactctttggaatttag--agttatatggagacttgttttagtattttctggtatcttttatgttttattagccatt--tacattctatgccagGGGGGATTTATTGATGATTTTCTTTCTCATTTGATGTGTTGCTGCTGTGCCCTTGTGCAAGAAAGGCGAGAAGTGGAGATCCATGGGGTTGAAG

upper sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G23240.1 (Glycine max), 3'ss of exon 7
---tttgagattctcccacaatctaatcattaacaggtagctttagtgtcgcatgtttaatttccttgaatattttgcttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG------
    |||   | |||     |  | |   |||  | | ||  ||  | |  ||| ||  | |  |||  || ||||  |    |||  |   |||| || ||||| |||||  |||||||||| || || ||| |||||||||| |||||||||||||| |||||| || ||||||||||||||||||| ||| | |      
aaggttgtagtactctttggaatttagtgtta-tatggagacttgttttttcattttctagtatcttctatgttttattagccattgaca--ttctatgccagGGGGGCTTTATTGATGATTTTCTTTCTCATTTGATGTGTTGTTGCTGTGCCCTTGTGCAAGAAAGGAGAGAAGTGGAGATCCGTGGTGTTGAAGGTATGA

upper sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G17780.1 (Arabidopsis thaliana), 3'ss of exon 7
tttgagattctcccacaatctaatcattaacaggtagctttagtgtc-gcatgtttaatttccttgaatattttgcttcttatt-atccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG---
                               |  |   || |   ||  | |  ||||  || |   ||  |  | || |||   ||  |||   ||  |||||||| |   |||| || ||  | |||||||| |||||||| || ||||||||||||||||||  | ||||||| ||||| | | | | || |    
-----------------------------gtacatcaattaaacctctactttcttaaggtcgt--gatgctaaggtttttacggatgtcttgaatttgcagGGAGGGTGCATTGACGACTTTTTGTCACATCTAATGTGTTGTTGTTGTGCCCTTGTCCAAGAACTGAGAGAAGTCGAGATTCATCGAGCTTCTTACG

upper sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G17780.3 (Arabidopsis thaliana), 3'ss of exon 7
tttgagattctcccacaatctaatcattaacaggtagctttagtgtc-gcatgtttaatttccttgaatattttgcttcttatt-atccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG------
                               |  |   || |   ||  | |  ||||  || |   ||  |  | || |||   ||  |||   ||  |||||||| |   |||| || ||  | |||||||| |||||||| || ||||||||||||||||||  | ||||||| ||||| | | | | || |       
-----------------------------gtacatcaattaaacctctactttcttaaggtcgt--gatgctaaggtttttacggatgtcttgaatttgcagGGAGGGTGCATTGACGACTTTTTGTCACATCTAATGTGTTGTTGTTGTGCCCTTGTCCAAGAACTGAGAGAAGTCGAGATTCATCGAGCTTCTTACGGTA

upper sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G35920.3 (Arabidopsis thaliana), 3'ss of exon 7
tttgagattctcccacaa-tctaatcattaacaggtagctttagtgtcgcatgtttaatttccttgaatatt----ttgcttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG
    | ||||      || | | ||  || |  | | |   | |    |  | |   | |   |  |   |     |   | |||| | |    |  |||  |||||||| ||  |||| ||||| || || ||| | |||||||| |||||||||||||| ||||||  | ||||||| ||||| |||||||  ||||
---aaaattcagtagtaactatcatggttga--gattgaaatggctatgtttatgccactcaatgtagagtcggaatgaatgcttaatgttttctgatttcgcagGGAGGATTCATTGACGATTTTCTATCTCATGTAATGTGTTGTTGCTGTGCCCTTGTACAAGAACTGAGAGAAGTTGAGATTCGTGGGGCATATG

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|110372614|gb|EC936798.1|EC936798
EST:     GCTATACTTGCTGTATCAGAAGGAAGCTTCGCAACATGTTGAACATCACG                         GGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCC
genomic: GCTATACTTGCTGTATCAGAAGGAAGCTTCGCAACATGTTGAACATCACGgtaactcctc ... tctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCC
EST: gi|352768563|gb|FQ467519.1|FQ467519
EST:     GCTATACTTGCTGTATCAGAAGGAAGCTTCGCAACATGTTGAACATCACG                         GGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCC
genomic: GCTATACTTGCTGTATCAGAAGGAAGCTTCGCAACATGTTGAACATCACGgtaactcctc ... tctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCC
EST: gi|352769201|gb|FQ471149.1|FQ471149
EST:     CCTATACTTGCTGTATCAGAAGGAAGCTTCGCAACATGTTGAACATCACG                         GGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCC
genomic: -CTATACTTGCTGTATCAGAAGGAAGCTTCGCAACATGTTGAACATCACGgtaactcctc ... tctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCC
EST: gi|30299868|gb|CB976662.1|CB976662
EST:     GCTATACTTGCTGTATCAGAAGGAAGCTTCGCAACATGTTGAACATCACG                         GGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCC
genomic: GCTATACTTGCTGTATCAGAAGGAAGCTTCGCAACATGTTGAACATCACGgtaactcctc ... tctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcatgtttaatttccttgaatattttgcttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG
      gtttaat  putative branch site (score: 4)
                      tattttgcttcttatt  putative PPT
       tttaatttccttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgagattctcccacaatctaatcattaacaggtagctttagtgtcgcatgtttaatttccttgaatattttgcttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - -ttctccc
- - - - - - - - - - - - cattaac
- - - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttccttg