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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgacttgctcttcttttttttttaatcatatttcacctatcaccaactggggtaactgaattattttttcttgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT

Basic information

species Vitis vinifera
transcript Vv19s0015g01950.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 4
gttcgacttgctcttcttttttttttaatcatatttcacctatcaccaactggggtaactgaat-tattttttcttgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT
       | | | || | || | | |  |  | ||||    |  |     ||     ||| ||  |   |    ||| || |||||| ||||| ||||| ||||| || |||||||||||||| ||||| |||||||||||||| || ||||| || |||||||
-----gttagtttttttcttgtgtgtgttgctttttccataaataatttttgttaagacttaacgttagtacgtttgatttaaagACTGTAGAGGCAGAGAGGATATCTGTTGATCATGTTGCCCATCTCAAACCATCTGATGGTGGCTCTGCGGCGACTCAAT

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
gttcgacttgctcttcttttttttttaatcatatttcacctatcaccaactggggtaactgaattattttttcttgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT
||  |  || | | |  | ||| | |||  |||| |    | |    |||            ||| | | | |||| |  |||||| ||||| || || ||||| || || || |||||||| ||||| |||||||||||||| ||||| || |||||||| |
gtaagtatttccccttctgtttgtctaactatatattgttttttcttaac------------att-tgtatgcttgata-aaagACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 4
--------------gttcgacttgctcttcttttttttttaatca-tatttc---acctatc-accaactggggtaact---gaattattttttcttgtttc---aaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT
               |||  ||  | ||| |    |||| ||||| | ||||   |   ||  |   ||| || |  |     |      |  ||||| ||     ||||| || ||||||||| |||| |||||||||||||||||||||||||| ||||||||||| ||||| ||||| || ||||
gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaattaattgattgacttggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 4
--------------gttcgacttgctcttcttttttttttaatcatatttcacctatca------ccaactggggtaactgaattattttttct--tgtttc---aaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT
               |||  ||  | ||| |    |||| |||||   ||   | || |       ||  |||  |  ||    | |   | ||  || ||     ||||| || ||||||||| | || |||||||||||||||||||||||||| ||||||||||| ||||| ||||| || ||||
gttgggttttatgacttctgctatcccttttcacattttaaatcactgtttctcaattaattgattcacttggattcccttctctctccctcctcatgctttgctgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------gttcgacttgctcttctttttttt-ttaatcat------atttcacctatcaccaactggggta-actgaattattttttcttgtttcaaa-------gACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT
                     | | | |   | || |||||||| | || |||      |||| | ||||         | ||| | ||| | |  ||||   || | | |       ||| || ||||| ||| |||| ||||||||||||||||| ||||||||||||||||| ||||| || || ||||| || |
gtctgtgcttaagtttgattctgcaaataattttttttttttttgtcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 4
----------gttcgacttgctcttcttttttttttaatcatatttcacctatcaccaactggggtaactgaattattttttcttgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT
             | ||||| |||    | | | |   | ||||   |     |    | |    |  |  ||| ||| |       | ||  ||| || ||||| ||||| || || |||||||||||||| |||||||| |||||||||||||| || ||||| ||||| |
gtatgtgtttaggccacttgatctgtaatctatctatgtgatatgagagtggactttcaataacattgc--aatgattgtaaacgcgtgca--gACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT

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|110713432|gb|EE089350.1|EE089350
EST:     TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG                         ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCA
genomic: TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAGgttcgacttg ... tgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCA
EST: gi|71856758|gb|DT005813.1|DT005813
EST:     TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG                         ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCAT
genomic: TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAGgttcgacttg ... tgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCAT
EST: gi|110363635|gb|EC927237.1|EC927237
EST:     TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG                         ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCA
genomic: TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAGgttcgacttg ... tgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCA
EST: gi|110368023|gb|EC931983.1|EC931983
EST:     TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG                         ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCA
genomic: TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAGgttcgacttg ... tgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCA
EST: gi|349818410|gb|FQ409185.1|FQ409185
EST:     TAGATGGGATTCCCCAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG                         ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCCTAAACCA
genomic: TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAGgttcgacttg ... tgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCA
EST: gi|110684768|gb|EE062427.1|EE062427
EST:     TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG                         ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCA
genomic: TAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAGgttcgacttg ... tgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatttcacctatcaccaactggggtaactgaattattttttcttgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT
                       gggtaac  putative branch site (score: 3)
                                  ttattttttcttgttt  putative PPT
                                aattattttttcttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgacttgctcttcttttttttttaatcatatttcacctatcaccaactggggtaactgaattattttttcttgtttcaaagACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC