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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattatctatcaatgattgcacattcttgaaaaatatcttatacaaaaactcatcctgtttcaatgtattggttggacatggggttgaactttgga...

Basic information

species Vitis vinifera
transcript Vv12s0035g01060.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G138676_T02 (Zea mays), 5'ss of exon 9
CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattatctatcaatgattgcacattcttgaaaaatatcttatacaaaaactcatcctgtttcaatgtattggttggacatggggt-tgaactttgga-
 || |||||||||||||||| ||||| || |||||||||||||||||||||||||| ||  ||  |  |      |    | |        | || | |         |         |  |||||    | ||| |  | || |  ||| | 
GCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAGgtgatttt--cttacggtatccatatgaccatatctctactgttttgctgccttcttttgcaccatgacatattga---ggcatagcatctgcatcttgcag

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA12G28730.2 (Glycine max), 5'ss of exon 9
CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgat-attatctatcaatgattgcacattcttgaaaaatatcttatacaaaaactc---atcctgtttcaatgtattggttggacatggggttgaactttgga
|| |||||||||||||| || ||||||||||| |||||||| ||||||||||| |  |||  | ||| ||  ||    |||  |    | |    ||| | | |       ||  |  ||  |   |||   || |||  |  || |  |     
CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggatttaccatccatttttttcaattaatctggatttggctatcctagattatgaaatgtttcttttagacattatatgtacaatgaattcagttg----

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA16G00400.1 (Glycine max), 5'ss of exon 8
CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgat-attatctatcaatgattgcacatt--cttgaa--aaatatcttatacaaaaactcatcctgtttcaatgtattggttggacatggggttgaactttgga
|| |||||||||||||| || ||||||||||| |||||||| ||||||||||| |  |||  | ||| ||| ||    |||    || |   | ||||||| |  |  |   || || |||  |  |  |   || |||     ||     |||| 
CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggatttaccatccatgtttttcaattaatctggatttactatcttagatgatgaaatattctttttagacatcata--tgtacagtaaattcgg--ttgg-

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 5'ss of exon 9
CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattatctatcaatgattgcacattcttgaaaaatatcttat----acaaaaactcatcctgtttcaatgtattggttggacatggggttgaactttgga
||| |||||||||| || |||||||||||||| || ||||| ||||| |||||    ||   ||| |||  ||  |  || |  ||||  |||   |    | |||     |   | ||| |     || |||  || | |     |  |   | 
CCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAGgtagcctt--ttattaattctttaaatttatctaaaatcatcaagtcctgataaagtgataagttcttttagaacttttgttt-acgtagcagacaggtgcag-

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 7
CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattatctatcaatgattgcacattcttgaaaaatatcttatacaaaaactcatcctg----tttcaatgtattggttggacatggggttgaactttgga---------------------------------------------------------------------------------------------
|||||||| ||||||||||| ||||| |||||| | || || |||||||||||    |||  |||    |||          || |     |||    || |      | |||    ||    | | |  ||| || |||  ||    | ||| |                                                                                             
CCTTTGTTCCCTGGAGAAAGTGGAGTCGATCAATTGGTGGAAATCATCAAGgtagc-ttacatatggtagatgttgaggaagtgcaggg-gtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttag

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 5'ss of exon 7
CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatat-tatctatcaatgattgcacattcttgaaaaatatcttata---caaaaactcatcctgtttcaatg-tat-tggttggacatggggttgaactttgga-------------------------
||||||||||||||||| || ||||| |||||| | || || ||||||||||||  |   |  |   |    |||    |     |       ||| |           |     |||  |  || ||| | ||| |   |||   |||   | |                           
CCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAGgtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcag

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattatctatcaatgattgcacattcttgaa----aaatatcttatacaaaaactcatcctgtttcaat-----gtattg-gttggacatggggttgaactttgga-----------------------------------------------------------------------------------
|||||||| |||||||||||||||||||||||| | || |||||||||||||| || ||||  ||    || || |      || |    || |   || |||  |   |     ||| || ||     ||||||  ||  |  |   | ||     ||                                                                                     
CCTTTGTTCCCTGGAGAAAGCGGAGTTGATCAATTGGTGGAGATCATCAAGgt-atgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacag

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|30126156|gb|CB911495.1|CB911495
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAT
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
EST: gi|110726124|gb|EE101641.1|EE101641
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
EST: gi|27580396|gb|CB003091.1|CB003091
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAT
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
EST: gi|161715603|gb|FC067769.1|FC067769
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
EST: gi|27579322|gb|CB002017.1|CB002017
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAT
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
EST: gi|156736132|gb|EV240253.1|EV240253
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
EST: gi|27581595|gb|CB004290.1|CB004290
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAT
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
EST: gi|27581007|gb|CB003702.1|CB003702
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAT
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
EST: gi|30130728|gb|CB916067.1|CB916067
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAT
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC
EST: gi|27579129|gb|CB001824.1|CB001824
EST:     CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG                         GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAT
genomic: CTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattat ... tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAGgtgatattatctatcaatgattgcacattcttgaaaaatatcttatacaaaaactcatcctgtttcaatgtattggttggacatggggttgaactttgga

- - - - -  TGGAGA
- - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaaa