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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggttatagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG

Basic information

species Vitis vinifera
transcript Vv10s0116g00360.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 12
gttggttcttcattccgcttaatcattt-ttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggttatagtagt--taataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG
||  |  |   ||    |    ||| || ||| |      |||  |    |||          |||    |  |       || ||  ||  |      | ||      | | || |||     | | |  |||| |    |  |   | || |  |||| | |       |  ||||||||| || ||  ||||||| || ||||||||||| |||||||||||||| ||||| || || |||||||| |||||||| || |
gtatgcacactatagttccctgtcacttgttggatacccagattggaa--cctaagaacgggctttgtggaagtga-----tgtttgcagcatgt---ttgtttacgaaccagcgcaggcagatgaacttctaatgatatgatcatgctcttatgtttgtatttt------tactcagGTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACG

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 5
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggttatagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG
                                                                 | || |||      |  ||   |||  ||  | | |||| ||| |  |        |  | ||   ||  || |  |   ||| ||   ||| | |  || |  ||| ||||||| || ||  | |||||||| ||||||||||||||||||||||| || ||||| ||| | |||||||| |||||||| || |
--------------------------------------------------------------acctacagtattaggagcatctgggagatgtctta-tattgtgattgtggc--------tgatcgtatgtacttgcatga---tttggtcgctgtcttttttctttgctt-agGTTGGCAACCTTGCGGCTCCAGTAGAAGAATGGACTGTTGGTGGAACAGCATTGACATCACTGATGGATGTTGAGAGGAGGCACG

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 12
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggttatagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG
                                                                       |     ||  |  ||    |   | | |||| | ||    | |    | ||  ||  || |   || |  |  |  | |   |  ||| |  |  |    ||||||||| || ||  | |||||||||||||||||||||||||||||||| || || || ||| | |||||||| |||||||| || |
-----------------------------------------------------------------------acagtgttaggaatacctgggagata-tcttataatgtgtttgtgactgatcttatgtact---tgcatgatttaatcgctgtcttttttttttcttggctcagGTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 10
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggtt--atagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG
                      |  |     | ||| |   |   |||||  |  |  |||  ||   ||||| || |   | ||   |  || ||    |   | |  |    || |||   || || |       | |||  | |||||| |  || |  | ||  | |  ||||||||| ||| ||| |||||| || ||||||||||||||||||||||||||  | |||||||| ||||| ||||||||||||||||
--------------------gtttgtgccaatgcttctcatt--atcttctctaatcatcaaatta--aatatttcttctagatt---ggttttaatgattgactgtggttgaaaatgtttcgtaatactggggccatcaactcaatttttggatctgcta-tgatatttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggtt--atagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG
                      |  |   | | || ||       |||||   |  |   |||      |||| || |   | ||   |  || ||    |  || |  |    || |||   || || |   |   | |||  | ||||| | |||   | | ||  | |  ||||||||| ||| | | |||||| || ||||||||||||||||||||||||||  | |||||||| ||||| ||||||||||||||||
--------------------gtttgtgcctatgctcttcacattatcttctaatcatcaaatta----gatatttcttctagatt---ggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttt-tgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 12
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggttatagtagttaa-taactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG
                | ||   | | | |  |    || |||  |     | |  ||  || | ||| | || |  |  || | || || |  |     |||  ||| | |      || || || | || | ||  | | |  | |||  ||||   | | |   | |  ||||||||||||| | | |||||||||  |||||||||||||||||||||||||  | || ||| | ||||||||||||||||| ||||
----------------gtttgtgcttctctacatgccttaatcttttgatatctacttaaatatctcctagat-tggtattgataattgattgta---ctttgaaattgtgtttgtt-ttgtaatattgaagtcaccaacctagttcttt--aatttgctttgacattttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 12
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattct-atcgaaggttatagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG
                | ||   | | | |  |    || |||  |     | || ||  || | ||| | || |  |  || | || || |  |   |    || | ||  |       ||| | ||| |  |||  |       || | |||||  || | ||  |    ||||||||  ||| | | |||||| || ||||||||||||||||||||||||||  | || ||| | ||||||||||||||||| ||||
----------------gtttgtgcttctctacatgccttaatcttttgatatcttcttaaatatctcctagat-tggtgttgataattgattgtactttgaaattgtgcttgttttgcaatattgaagtcaccaacctag------ttatttaatttgttttgatatttggatcagGTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATG

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggttatagtagttaataactgaacaaactttttgt---aattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG
                                                                      | | |  | |  | | |  | |  || || || |   ||| | ||   | ||||   ||  |||   |  |     || |    |  ||  |    | ||     |||||||||||  || ||||||| || |||||||||||||| ||||| |||||  | ||  | || |||||||| ||||||||||| |
---------------------------------------------------------------------gtttgtactccaccatttccactaaaatctgttttccatctgt-gatcataatagcctttggtaaactagtatgtgcttagaatgagatgagttaacttattggcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG

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|87583926|gb|DY473286.1|DY473286
EST:     TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAGACTGGGCTGATATCATCG                         GTTGGGAATCTGACTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
genomic: TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGGCTGATATCATCGgttggttctt ... atgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
EST: gi|161717766|gb|FC066590.1|FC066590
EST:     TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGGCTGATATCATCG                         GTTGGGAATCTGGCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
genomic: TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGGCTGATATCATCGgttggttctt ... atgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
EST: gi|110699977|gb|EE077493.1|EE077493
EST:     TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAGACTGGGCTGATATCATCG                         GTTGGGAATCTGACTGCTCCAGTTGAA-AATGGACTGTTGGTGGAACTGCC
genomic: TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGGCTGATATCATCGgttggttctt ... atgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
EST: gi|77584856|gb|DV221506.1|DV221506
EST:     TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAGACTGGGCTGATATCATCG                         GTTGGGAATCTGACTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
genomic: TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGGCTGATATCATCGgttggttctt ... atgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
EST: gi|110720557|gb|EE096583.1|EE096583
EST:     TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAGACTGGGCTGATATCATCG                         GTTGGGAATCTGACTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
genomic: TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGGCTGATATCATCGgttggttctt ... atgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
EST: gi|27581975|gb|CB004670.1|CB004670
EST:     TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAGACTGGGCTGATATCATCG                         GTTGGGAATCTGACTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC
genomic: TTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGGCTGATATCATCGgttggttctt ... atgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG
        taataac  putative branch site (score: 1)
                                              tgtcttc  putative PPT
                    aaactttttgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggttatagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA