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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgtaattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT

Basic information

species Vitis vinifera
transcript Vv17s0000g01550.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 21
cagttcatcaggctgaacagagcacttc-aaatactatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgtaattgttcca--tgtgc-agCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
   |      || ||     |  ||||    ||| |   |  | || || |      || | |  ||  ||||   |||  ||| |||| |     ||||| |||| || || || ||| | || |||||||| ||||| ||||| |||||||||||||| || ||||| ||||| || |||||||| || ||||| ||||| |
-gttatgaatggatgggggtactacttttggatagtgg-aattttttatttccatt-ttatttgatagtgaactgacttt-tgttattgcttatgttgtgccagCCATGTAAAGGAATATTACTTTTTGGCCCGCCTGGTACAGGAAAGACAATGCTTGCCAAAGCTGTGGCTACAGAGGCTGGTGCGAATTTCATAAATATAT

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
cagttcatcaggctgaacagagcacttcaaat--actatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgtaattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
|  |   |  ||  | |  ||| | |  |  |   ||| |   | ||     ||  | |  | |  |||  |       | ||  |  ||||  |  |||||||||||||||| ||| | || ||||| || ||||| || || || || |||||||||||||| || || |||||||| ||||| |||||||| || || |
ctatattttgggacggatggagtattatatgttggctacctaattttctctatttaagtcctatcttaaaaattgcctctggtaaatctgtt--acttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatctta--gtgtaattgttccatgtg----cagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
      ||     |   |  |    || |         ||| || || |    |  ||   |   |   | | | ||||   |||   | ||| ||       ||||| || || || ||  | || |||||||| ||||| || || ||||||||||||||||||||||| || ||||| |||||||| || ||||| || || |
------atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 21
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgt-aattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
      ||||     |  | |  | |   ||   | |   | ||   |  |   | |  |  ||      |   | | | ||| ||||        ||||||| |||||||| || ||  ||||||| |||||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||||||| ||||
gtaaaaatcacaaacattaaaataatgtgaa-gttgtagcccatctcttgtcaaattattaatcatttttattttatgattgtgaattaccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
cagttca--tcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgt-aattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
 |||  |  |||     |  | || | |   ||   | |  ||  |   |  |   |||| |  ||      | | | | | ||| |||||       ||||||| |||||||| || ||  ||||||| |||||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||||||| ||||
-agtaaaaatcacaaacattaaagtaatgtgaa-gttgtaggccttctcttgtca-aattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgc--aattgtgttctaaggaacaatcttagtgt--aattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
|| || || |  || || | |  | ||  |  || |||     ||| |||||    || | |  || |       ||||        ||||      ||||||||| ||||| || || ||  ||||||| ||||||||||| || || ||||||||||| |||||  ||||||||||||||||||| ||||||||||| ||||
caattaataaatct-aatata--attttgatgaccatctaac-ttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 17
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgc--aattgtgttctaaggaacaatcttagtgt--aattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
|| || || |  || || | |  | ||  |  || |||     ||| |||||    || | |  || |       |||| |   |  ||||      ||||||||| ||||| || || ||  ||||||| ||||||||||| || || |||||||| || |||||  | ||||||||||||||||||||||||||||| ||||
caattaataaatct-aatata--attttgatgaccatctaac-ttgctctttatcaaaatattatccattctgttatctcaactttgaattaccttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: PP1S3_184V6.1 (Physcomitrella patens), 3'ss of exon 17
cagttcatcaggctgaacagagcacttcaaatactat--cagctattgatctttgcaattgtgttctaaggaacaatcttagtgtaattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
  |   ||  |         |    || |  || | |  |   |||    | |   |||  | || | |     |||     | |  |   |   ||||||||| ||||  ||| |  | |||||||| || || || ||||| ||||| ||| | |||||||||||||| |||||||| || || |||||||| || ||||
--ggctattggatgatttttattcgtttatttattttgacgattatgatgcgtattaatattattattattttgaatgcacatctcttctctgtttgtgcagCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTT

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgtaattgttccatgtg-cagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
                                               ||| ||   |||| |  |         |||| || |||    |  || || |||||||| | |||| ||||  ||||||| || || ||||| || ||||| |||||||||||||| |||||||| || ||||||||||| |||||||||||||
----------------------------------------------gtctgtgtgtttgt-tatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgtaattgttccatgtg-cagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
                                               ||| ||   |||| |  |         |||| || |||    || || || |||||||| | |||| ||||  ||||||| || || ||||| || ||||| |||||||||||||| |||||||| || ||||||||||| |||||||||||||
----------------------------------------------gtctgtgtgtttgt-tatttgctttttttctttgtctaacgaatctatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

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|37186767|gb|CF606120.1|CF606120
EST:     TGCTTCCACTACAAAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAG                         CCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATG
genomic: TGCTTCCACTACAAAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAGgttttcacat ... ccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATG
EST: gi|30255057|gb|CB971504.1|CB971504
EST:     GCTTCCACTACAAAGGCCTGAACTTTTTTGCAAGGGGGA-TCNAACCAAG                         ACTTGCAAGGGCATAACTTCTATTTGGCCCCCCTGG
genomic: GCTTCCACTACAAAGGCCTGAACTTTTTTGCAAGGGGCAATT-AACCAAGgttttcacat ... ccatgtgcagCCTTGCAAGGGCATA-CTTCTATTTGGCCCCCCTGG
EST: gi|110720420|gb|EE096327.1|EE096327
EST:     TGCTTCCACTACAAAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAG                         CCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATG
genomic: TGCTTCCACTACAAAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAGgttttcacat ... ccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATG
EST: gi|110711745|gb|EE088578.1|EE088578
EST:     TGCTTCCACTACAAAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAG                         CCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACANGCAAGACAATG
genomic: TGCTTCCACTACAAAGGCCTGAACTTTTTTGCAAGGGGCAATTAACCAAGgttttcacat ... ccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctttgcaattgtgttctaaggaacaatcttagtgtaattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT
 tattgat  putative branch site (score: 3)
                                        ttgttcc  putative PPT
                                     taattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatcttagtgtaattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - gaacaga
- - - - - - - - - - - - - -caaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaacaa