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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacttgtccctgaattctcatttttgcatctttacatctggtcacttacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG

Basic information

species Vitis vinifera
transcript Vv18s0089g00350.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 19
-------------gtaagcacttgtccctgaattc---tcatttttgcatctttac---atctggtcac--ttacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
                  || ||||  |   | ||     ||||||  | ||  |    |  ||||||   || ||| || |  | ||| ||     ||  |   |||||| | || ||||||||||| |||||||| |||||||| |||||||||||| | ||||||  ||| ||
gtttacatttgaacctcacaattgtttcaacagtcatactattttttaaactcaatttaacatggtcatagttgcaattgtt--attat-tgtctttttcatgatcagGCAATCGTACTTTGCCAAGTGGAGAAAGCAAAGGAAGATATGCTAAATCAGCTCTACAGCAAAATAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os08g32920.1 (Oryza sativa), 3'ss of exon 19
-gtaagcacttgtccctgaattctcatttttgcatctttacatctggtcacttacaaatgcttgaat--atgtgatcgat--tggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
  ||||||  |    |||   |||   ||  || |   |   |||   |  ||  |  | |||| ||  || | || |||  || |  |||||| || |||||||||||||||||||| || ||||||| |||||| |||||| | || |  || || ||
gttaagcatgt----ctggtgtcttgcttaagctttcctg-gtct---cctttctagcttcttgcattaatatcattgatcctgttgagCAGGCTGTGGTTCTTTGCCAAGTTGAGAAGGCAAAGGAAGGCATGCTTAATCAGCTCTATACTTCGATAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 7
gtaagcacttgtccctgaattctcatttttgcatctttacatctggtcacttacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
||    | |  ||  | |||     |||      | ||  || ||     |  |||||  || | |   ||   |  |  |||  ||||  |||| || |||||||| |||||||| |||||||||||||| || ||| | |||||||| || ||
gttcatattgttctgttaatca--gtttaaatggccttgtatttg-----tgtcaaat-tttcattgcttgtctg--tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 19
gtaagcacttgtccctgaattctcatttttgcatctttacatctggtcacttacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
||    | | |||  | ||  |   |||      | ||  || ||     |  ||||| ||| | | | ||   |  |  |||  ||||  |||| ||||| ||||| |||||||| |||||||||||||| || ||| | |||||||| || ||
gttcatattggtctgtcaa--ccagtttaaatggccttttatttg-----tgtcaaattctt-attgtttgtctg--tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 19
gtaagcacttgtccctgaattctcatttttgcatctttacatctggtcactta-caaatgcttgaa----tatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
||||||   ||    | |  | |  | |||  ||  ||   || | |     |   |||||||||     | | || | | ||||||  ||||||||||| ||||| |||||||| || ||||||||||||||||| ||||| || || |||||  ||||
gtaagcttctgcttttaacattttctatttatataattttttcagtttttccagttaatgcttgatgcattttctggttgcttggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAATTATATAGCTCTGTCAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 19
gtaagcacttgtccctg--aattctcatttttgcatctttac--atctggtcactta-caaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
||||||   |||   |   | ||  |||||||  |  ||| |   | |   || |||     || |  | | | || | | ||||||  ||||||||||| ||||| |||||||| || ||||||||||||||||| ||||| || || |||||  ||||
gtaagcttctgtttttagcatttgccatttttataatttttccagttttcccagttaatttttgatgcattttctggttgcttggtttacagGCAGTTGTCCTTTGTCAAGTTGAAAAGGCTAAGGAAGACATGCTGAATCAATTATATAGCTCTGTCAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 19
---------------gtaagcacttgt---ccctgaattctcatttttgcatctttacatct-----ggtcacttacaaatgct--tgaat-atgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
               | ||   || |    | || |||| || | |     ||||| |   |     | |  ||     |||||  | |   ||||||        |   ||||| ||||||||||| ||||| |||||||| |||||||||||||| |||||  | ||||| || || ||
gtgaactatccttatgcaaaagctcgaaagctctaaattttcttgtccatctcttttctcttacagagattcctcggtcatgctactaagcgatgtgaattgaccatgaacagGCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
-----gtaagcacttgtccc-tgaattctcatttttgcatctttacat--ctggtcact-tacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
      ||  ||||| ||   |||||||| |  ||  |||    | ||  ||  ||| |   | |   | | | ||  |    || |  |   ||||| |||||||| || ||||| |||||| | |||||||||||||| |||||| | |||||||| |||||
gtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgact--tcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG

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|33402994|gb|CF208621.1|CF208621
EST:     GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAA                         GCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
genomic: GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAAgtaagcactt ... tggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
EST: gi|34364107|gb|CF405692.1|CF405692
EST:     GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAA                         GCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
genomic: GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAAgtaagcactt ... tggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
EST: gi|30251129|gb|CB968862.1|CB968862
EST:     GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAA                         GCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
genomic: GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAAgtaagcactt ... tggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
EST: gi|161714373|gb|FC063214.1|FC063214
EST:     GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAA                         GCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
genomic: GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAAgtaagcactt ... tggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
EST: gi|37185438|gb|CF604791.1|CF604791
EST:     GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAA                         GCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
genomic: GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAAgtaagcactt ... tggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
EST: gi|34364376|gb|CF405961.1|CF405961
EST:     GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAA                         GCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG
genomic: GTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAAgtaagcactt ... tggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttacatctggtcacttacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG
               cacttac  putative branch site (score: 2)
                  ttacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacttgtccctgaattctcatttttgcatctttacatctggtcacttacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA