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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaggtttcaatttttttagtacaagtttcattattttatgttcatgttcggttctataatgggatctcttttttttcctttgccttcatcttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGAAGTCAGCCGACCCTCCAAGGAGCTTGAG

Basic information

species Vitis vinifera
transcript Vv14s0083g01050.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g01050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G04320.1 (Glycine max), 3'ss of exon 1
ccaggtttcaatttttttagtacaagtttcattattttatgttcatgttcg-gttctataatgggatctcttttttttcctttgccttcatcttatgt-tagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGAAGTCAGCCGACCCTCCAAGGAGCTTGAG
  | |  ||| ||  | |||||    |||   |||  | | |  || | |     | || ||    | |  |  || | | || |  || ||  || |  ||||||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||||  |||   ||| |||||||||
-tatggctcatttggtgtagtaattcttttggtatggtttatg-atatccatacaccattatcaattttactagttcttcctttctctcctcgaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTGGAAGTCAGCAAACCTGGCAAAGAGCTTGAG

upper sequence: Vv14s0083g01050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G27670.1 (Glycine max), 3'ss of exon 1
ccaggtttcaatttttttagtacaagtttcattattttatgttcatgt-tcggttctata-atgggatctcttttttttcctttgccttcatcttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGAAGTCAGCCGACCCTCCAAGGAGCTTGAG
   |   ||  |||  | | ||   |||  ||   |   | | |||   ||   |  ||  ||  ||    | ||  || |||||  | | | | |  | ||||||||||| ||||| ||||| ||||| ||||||||||||||||| |||||||| | |  |||  |||| ||||| |||
-ttgacatccttttagtaattaattgttgtatgcatggttatccatacatcatcttcatggatttgactgttcttcctttctttgtgtacct-tgaaatcagCATGCTCAAAACACTTGAAAGGTACCAGAAATGCAGTTATGGTGCTGTGGAAGTTACCAAACCTGCCAAAGAGCTCGAG

upper sequence: Vv14s0083g01050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G06730.1 (Glycine max), 3'ss of exon 1
ccaggtttcaatttttttagtacaagtttcattattttatgttcatgttcggttctataatgggatctcttttttttcctttgccttcatcttatgt---tagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGAAGTCAGCCGACCCTCCAAGGAGCTTGAG
   | ||  |        | |   |    | || |  |||| | ||        |   |      |   |  || |||||||  || | ||||   |    ||||||||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||||  |||   ||| |||||||||
---gattagataacccagaatgtgaaacaccttttggtatggttatccatacaccatcaccaattttattagttcttcctttctctccttcttgaatctgcagCATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG

upper sequence: Vv14s0083g01050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G50900.1 (Glycine max), 3'ss of exon 1
ccaggtttcaatttttttagtacaagtttcattattttatgttcatgttcggttcta--taatgggatctcttttttttcctttgccttcatcttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGAAGTCAGCCGACCCTCCAAGGAGCTTGAG
    |||   |   ||||||||   ||   ||   |   | | |||      |  ||  | ||  ||    | ||  || ||||| || | | | |  | ||||||||||| ||||| ||||| ||||| |||||||| |||||||| |||||||| |||  |||  |||| ||||| |||
-attgttgataaccttttagtaattgtggtatgcatggttatccatacatcatcttaattgatatgactgttcttcctttctttgtctacct-tcaaatcagCATGCTCAAAACACTTGAAAGGTACCAGAAATGCAGCTATGGTGCTGTGGAAGTTAGCAAACCTGCCAAAGAGCTCGAG

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|33402815|gb|CF208442.1|CF208442
EST:     ATCATCTTCTCCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAG                         CATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAGgtcctctctt ... cttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGA
EST: gi|33405261|gb|CF210888.1|CF210888
EST:     ATCATCTTCTCCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAG                         CATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAGgtcctctctt ... cttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGA
EST: gi|110370316|gb|EC929381.1|EC929381
EST:     CCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAG                         CATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTAT-GTNGCAGTGG
genomic: CCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAGgtcctctctt ... cttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGT-GCAGTGG
EST: gi|110710966|gb|EE087623.1|EE087623
EST:     ATCATCTTCTCCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAG                         CATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAGgtcctctctt ... cttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGA
EST: gi|110398751|gb|EC965225.1|EC965225
EST:     ATCATCTTCTCCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAG                         CATGCTCAAGACACTTGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGA
genomic: ATCATCTTCTCCACCCGTGGAAAGCTCTATGAGTTCTGCAGCAGCTCAAGgtcctctctt ... cttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcggttctataatgggatctcttttttttcctttgccttcatcttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGAAGTCAGCCGACCCTCCAAGGAGCTTGAG
                    tctcttttttttcctt  CT-rich tract
                      tctttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaggtttcaatttttttagtacaagtttcattattttatgttcatgttcggttctataatgggatctcttttttttcctttgccttcatcttatgttagCATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGAAGTCAGCCGACCCTCCAAGGAGCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - -catgttc