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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctacaagcattgaatacatcaatattaaagatatactgttgtttccttcatgagaagagatgattatcaatctcagagtgcaattgtatccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACTGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA

Basic information

species Vitis vinifera
transcript Vv11s0118g00670.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
tctacaagcattgaatacatcaatattaaagatatactgttgtttccttcatgagaagagatgattatcaatctcagagtgcaattg--tatccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACTGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA
 |||  |   |        ||| | ||  |     | | |  ||   ||   | |    ||| |||    ||| || |   |  ||   | |   |   ||||| ||||||||||| || |||||||| || ||||| || ||||| ||||||||||| || ||||| ||||| |||||||||||| | || || ||||| |
-ctattatgttatcgctgctcatttttctaatcggagt-taattatattgtagtgctttgattattggatatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G028883_T01 (Zea mays), 3'ss of exon 2
--tctacaagcattgaat-acatcaa--tatta-aagatatactgttgtttccttcatgagaagagatgattatcaatctcagagtgcaattgtatccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACTGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA
    |   |   |  ||| || || |  ||||   ||||| |  || |||   ||  |       | |||||   ||| |   | |    || | ||   |   |||||||||| ||||| |||||||||||  | |||||||||||||| ||| ||||||| || ||||| ||||| |||||||| ||| | || || ||||| |
tacatgtgaatctgaaattacttctagctattttgagata-atcgtcgttgatttgctttctgatgttgattga-aattttgtatt----ttctgtctggtattagGCTCTTGTTGATGCCCCCGACATGGTTCGTTGCCAAATGAACTTCAAGCGGCTTTCCCTGACTGACATCAAGATTGACATTAAACGTGTCCCAAAGAAGA

upper sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G140116_T01 (Zea mays), 3'ss of exon 2
tcta-caagcattgaatacatcaatattaaagatatactgttgtttccttcatgagaagagatgattatcaatctcagagtgcaattgtatccctttg--cagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACTGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA
|||| ||| |  |   | | |     || |  || |    |  | |  || || |    ||   |||      ||||  |     ||| || |  |    ||||| ||||||||||| || || ||||| || |||||  ||||||| ||| |||| ||||| ||||| ||||| |||||||||||| | || || ||||| |
tctagcaacctatctctgcgttgcc-ttgattatttgtcttgctgtaattgattaatcaagc--attcaagccctcatcgccttgttgcattctgtgaaccagGCACTTGTGGATGCCCCTGATATGGTCAGGTGCCAGGTGAACTTCAAGCGGCTCTCACTTACTGACATCAAGATTGACATCAAACGTGTCCCCAAGAAGA

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|30134455|gb|CB919793.1|CB919793
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|37187972|gb|CF607323.1|CF607323
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|77580814|gb|DV219318.1|DV219318
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110429198|gb|EC995687.1|EC995687
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|71869827|gb|DT018882.1|DT018882
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|34319412|gb|CF372166.1|CF372166
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|27581709|gb|CB004404.1|CB004404
EST:     GGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: GGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110706377|gb|EE081851.1|EE081851
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|71865933|gb|DT014988.1|DT014988
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|34543799|gb|CF512031.1|CF512031
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|71880453|gb|DT029508.1|DT029508
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110361702|gb|EC925195.1|EC925195
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|77577814|gb|DV217659.1|DV217659
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|352795130|gb|FQ477240.1|FQ477240
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|32460994|gb|CD802168.1|CD802168
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|71885713|gb|DT034768.1|DT034768
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|351017039|gb|FQ424466.1|FQ424466
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110428543|gb|EC995018.1|EC995018
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110420972|gb|EC987259.1|EC987259
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110424520|gb|EC990883.1|EC990883
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110714507|gb|EE091492.1|EE091492
EST:     AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGGgtatgtgtga ... ccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcatgagaagagatgattatcaatctcagagtgcaattgtatccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACTGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA
                                          tatcccttt  CT-rich tract
                  attatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctacaagcattgaatacatcaatattaaagatatactgttgtttccttcatgagaagagatgattatcaatctcagagtgcaattgtatccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACTGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- -acaagca
- - - - - - gaataca
- - - - - - - - - - - - - -aaagata
- - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatctc