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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagtgcttaaacttattgtctcaacattacctttttcttcagatagtgacatattagtccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTG

Basic information

species Vitis vinifera
transcript Vv17s0000g02140.t01
intron # 33
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g02140.t01 (Vitis vinifera), 3'ss of exon 33
lower sequence: GLYMA07G11610.1 (Glycine max), 3'ss of exon 31
gtaagagtgcttaaacttattgtctcaacattacctttttcttcagat--agtgacatattagtcca-catatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTG
|||||  |  ||    | || |       | |   | | | || |  |  | |    | ||  |    || | || ||||||||| |||||||||||||||||||||||| ||||| |||||| |||||||||||||||| |||||  |||||||||||||||||||||||||||
gtaaggatcatttggttcatggctgtgcaactgattctcttttaaattttaatactgtttttctttggcacaaagAATGCAGAAAAGGGTGGATATGCTGTTGGAGCATTTAATGTATATAATTTGGAAGGAGTTGAGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTG

upper sequence: Vv17s0000g02140.t01 (Vitis vinifera), 3'ss of exon 33
lower sequence: AT1G18270.2 (Arabidopsis thaliana), 3'ss of exon 35
gtaagagtgcttaaacttattgtctcaacattacctttttcttcagatagtgacat-attagtccacata---tagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTG
|| ||  | |||   ||  || ||| | | | |  | | |||||  ||| |||  |  |   || |  ||    || |||||||||  ||||||||||| ||||||||||| || || ||||| ||||||||| | || || ||||| || || |||||||||||| | |||||||
gtgagtatcctt---ctcgttctct-agcttcatatatctcttctcatattgatgttgtctttctatgtaaaacagAATGCAGAAAAAGGTGGATATGCAGTTGGAGCATTTAACGTGTATAACCTGGAAGGAATAGAAGCTGTTGTAGCGGCCGCAGAGGAAGAAAATAGTCCTG
















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|349820359|gb|FQ403975.1|FQ403975
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|349819138|gb|FQ412032.1|FQ412032
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|349824597|gb|FQ413264.1|FQ413264
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|71870716|gb|DT019771.1|DT019771
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|71860468|gb|DT009523.1|DT009523
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|71887135|gb|DT036190.1|DT036190
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|30253243|gb|CB970794.1|CB970794
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|71890098|gb|DT039153.1|DT039153
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|349817092|gb|FQ399839.1|FQ399839
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACCAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|349808649|gb|FQ405793.1|FQ405793
EST:     AATCTTGGGTTCGTCCTCTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|30323090|gb|CD006352.1|CD006352
EST:     AATCTTGGGTTCGTCCTGTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|32247669|gb|CD713488.1|CD713488
EST:     AATCTTGGGTTCGTCCTGTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|349826605|gb|FQ418696.1|FQ418696
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|349824745|gb|FQ414603.1|FQ414603
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|30326313|gb|CD009575.1|CD009575
EST:     AATCTTGGGTTCGTCCTGTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|30130704|gb|CB916043.1|CB916043
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|30324336|gb|CD007598.1|CD007598
EST:     AATCTTGGGTTCGTCCTGTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|26257761|gb|CA808824.1|CA808824
EST:     AATCTTGGGTTCGTCCCTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAAGGGGTGGATATGC
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAA-GGGGTGGATATGC
EST: gi|32268416|gb|CD717575.1|CD717575
EST:     AATCTTGGGTTCGTCCTGTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|349820676|gb|FQ408505.1|FQ408505
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
EST: gi|349808888|gb|FQ406738.1|FQ406738
EST:     AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAA-GGGCTTCTTCTT                         GATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG
genomic: AATCTTGGGTTCGTCCTTTTAGACTTTCATCAACAAAGGGGCTTCTTCTTgtaagagtgc ... ccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtctcaacattacctttttcttcagatagtgacatattagtccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTG
                  tttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagtgcttaaacttattgtctcaacattacctttttcttcagatagtgacatattagtccacatatagGATGCAGAAAGGGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC