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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaaaaaagaaaagattgaactctccctttatgaaatttaatgtcatgagaatcttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT

Basic information

species Vitis vinifera
transcript Vv17s0000g05070.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g41310.1 (Oryza sativa), 3'ss of exon 1
-----ccaaaaaaagaaaagattgaactctccctttatgaaatttaatgtcatgagaatcttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT
       |  ||     ||   |||  | | || |    |||  |  |   ||  | || |  |  | | |  | |   |  ||  ||| |  ||   | |||||| || |||||| ||||||||||| | || || || || ||||||||||||||  ||   |||||||||||||| ||||||
atgcatgattaaccatcaaagatgagatgtgccctaccaaaacgttcttcaatctggatgt--atcactaaattctgacttgtttcttgatacat---tatgcagAGGCATACGATCCGCTTGATCCAAATGGGAACATAACAATCAAGTGGGATGTGCTGCAATGGACTCCAGATGGATATGTT

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G32130.1 (Glycine max), 3'ss of exon 1
-ccaa--aaaaagaaaagattgaactctccctttatg-aaatttaatgtcatgagaatc--ttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT
  |||   |     ||| || || ||||   ||  |  || ||| |   ||| |  ||   || | ||||     ||  || ||| |||  ||    |||  ||||||||||| ||| |||||||||||   |||||||| || ||||| |||||||| || |||||||| |||||||| ||||||
agcaattgagtgagaaaaatagagctctgatttgttataagttttactccataaagattaattcaaaatt----catcaatatttttttcttgttcattt--gcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTT

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G22410.1 (Glycine max), 3'ss of exon 1
--ccaaaaaaagaaa-agattgaactctccctttatgaaa--tttaatgtcatgagaatc-ttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT
    |   |  || | | || || ||||   ||  |||||  |||| | |   |||| |  || | ||||||   ||   |||| |||       |   | |||||||||||| ||| | ||||||||    |||||||| || |||||||||||||| || ||||||||||||||||| ||||||
aagaattgagggagatatatagagctctgatttgttgaaaaatttactctatagagattaatttaaaattgatcaatatttcttgctt------gttcatttgcagAAGCCTATGATCCACTTGATCCTACCGGAAATATAACAATCAAGTGGGATGTCATTAGCTGGACTCCAGATGGCTATGTT

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 1
--ccaaaaaaagaaaagattgaactctccctttatgaaatttaatgtcatgagaatcttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT
    | ||     |  | || |    |  ||||   |||        |     |    | |   || |  || |  |   | |||  ||  | | | | ||||||| || ||| | ||||||||| | ||||||||||| ||||| |||||| | || || ||||| || ||||||||||||
tataagaagccttaggggttcattgattactttgccaaacccctctccccttcatatattaattttaatttaattttgagtttttc-tgtttatcttt-cagAAGCTTATGATCCACTTGATCCATATGGAAATATCACAATCAAATGGGATATCATAAGTTGGACCCCTGATGGTTATGTT

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
ccaaaaaaagaaaagattgaactctccctttatgaaatttaatgtcatgagaatcttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT
                      | ||||  | |    || |     ||   ||| ||||   || | || ||  | ||| | |            | ||||||| || ||| | ||||||||| | ||||||||||| ||||| |||||| | || |||||||| || ||||| ||||||
---------------------gtatccccctctccccttca----tatattaattttaat--tttaagtttttctgtttatct------------ttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
--ccaaaaaaagaaaagattgaactctccctttatgaaatt-taatgtca-tgagaatcttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT
   ||||  ||  ||  | |    |     || | | |||   ||||||  || | |||   | ||   | ||  | |  |||    |||  ||  || ||||||||| || ||| ||||||||||||| || || || || || || |||||||| |||||||||||||| ||||| ||||||
ctacaaaccaaataattagtagttttaagattgaagcaatcacaatgtcggtgtggatcaggataaacaaagttctgactttt----ggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT

upper sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S44_119V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------ccaaaaaaagaaaagattgaactctccctttatgaaatttaatgtcatgaga----atcttaagaattgaggtatt-------catctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT
                ||    | |  |  ||    ||    | ||   |  | |   ||  || ||    || ||  || ||    | ||       ||||| |||||      |||| | |  | ||  || ||| |  ||||||| |||||||| ||||||||||| ||||||||  |    |||||   ||| || ||    
gtgagcatcttgtttgcattctacggtagcatctggcttcttccttcgaatctgtcgcgtattgtgagcgtattttcggagttcgtatgttgtaataacatctatcttt--caactgttgcagATGCAGGATATGATCCAATTGATCCTGAGGGAAACATCACCATCAAATGGGATGTTGTTGAGTGGACAGGAGACGGGTACCGG

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|110365645|gb|EC928981.1|EC928981
EST:     CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAG                         AAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
genomic: CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAGgtgatgaccc ... gtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
EST: gi|110709853|gb|EE085677.1|EE085677
EST:     CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAG                         AAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
genomic: CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAGgtgatgaccc ... gtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
EST: gi|110711294|gb|EE087628.1|EE087628
EST:     CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAG                         AAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
genomic: CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAGgtgatgaccc ... gtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
EST: gi|110709374|gb|EE084778.1|EE084778
EST:     CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAG                         AAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
genomic: CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAGgtgatgaccc ... gtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
EST: gi|33407966|gb|CF213593.1|CF213593
EST:     CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAG                         AAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
genomic: CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAGgtgatgaccc ... gtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
EST: gi|110713068|gb|EE088664.1|EE088664
EST:     CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAG                         AAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
genomic: CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAGgtgatgaccc ... gtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
EST: gi|110712428|gb|EE090037.1|EE090037
EST:     CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAG                         AAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG
genomic: CGCCATTTTGCTTGTGTTGTTGTTTTCTTGCTCCATTTTCACTTCTACAGgtgatgaccc ... gtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgagaatcttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT
                                            tgtttct  CT-rich tract
          ttaagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaaaaaagaaaagattgaactctccctttatgaaatttaatgtcatgagaatcttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- aaaaaaa
- - - - -gaaaaga
- - - - - - - - - - -ctctccc
- - - - - - - - - - - - - - - - - - - - - - -catgaga