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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgtttatttgtctttacatgacaattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG

Basic information

species Vitis vinifera
transcript Vv04s0044g02020.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
aatctgtgttaacatggagtgtgagatgtcttgttggggcttact-tattgtgataatgtttatttgtctttacatgacaattttaaaactctatctg----cagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
        ||||    || |     |  |||     |  |  ||| |||  | |    |  | |  |    ||    |   | | |||| | |   ||    ||||||||||| ||||| ||||||||||| || |||||||| || || |||||  |||| || ||||| || ||||||||||||||||| ||||| ||||| |
-----taattaattaagaataaataaactctgcacagaacacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 20
aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgtttatttgtctttacatgacaattttaaaa------ctctatctg--cagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
      | ||      |    | |  |  ||||    |    | ||| |||    | |||| |||    ||| | |  |   || | |      |||| | ||  ||||||||||||||||| ||||||||||| || |||||||| |||||||| ||  |||| || ||| | || ||||| ||||| || || || || ||||| |
-----atatttctgctggaactaaagt-ccttgagctgttgcaattaatgt--ccaagtttgtttcatattaaagggaagaattgacagtgtttctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCAGGTTCAGCAGGAAAGCAATTGAAAGAAGCGCAAAGTATAAATAAATCTCTTTCTG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgtttatttgtctttacatgacaattttaaaa------ctctatctg--cagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
    ||||  |  || |  |   | |       |  ||||||  || | | | |  | |    ||    ||||  |  |   || | |      |||| | ||  ||||||||||||||||| ||||||||||| || |||||||| ||||| || ||  |||| || ||||| || ||||| ||||| || ||||| || ||||| |
----tgtgaaactattgcatcctaaacagtcctt--gggctt--ttgtagagtttgtttcacattacacttacggggaagaattgacagtgttcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G109420_T01 (Zea mays), 3'ss of exon 6
aatctgtgttaacatggagtgtgagatgtcttgttggggctt--acttattgtgataat--gtttatttgtctttacatga--caattttaaaactctatctg--cagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
  |  | |||     |         | | |  |  |  ||||   |  || | ||| |   | |    | |||    | ||    |   |    |||| | ||  ||||||||||||||||| ||||||||||| || |||||||| ||||| || ||  |||| || ||| | || ||||| |||                      
-gtacgcgttg---cgcgccactgcacgccgaggcgaagctttcgccgatggcgatgactagctggcctatctacgtacgaattgacagTGTTTCTCTGTTTGAACAGCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCAGCAGGAAAGCAATTGAAAGAAGCGCAAG---------------------

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 25
------aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgtttatttgtctttacatgacaattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
      ||  ||| |   |||    ||| |     |    |||  |  | | |||||         |  | ||   | | |      | |   | || || ||||||||||||||||||||||||||||||||||||| ||||| || ||||| ||| | || | ||| |||||||||||||| ||||| ||||||||| | ||||
cagggaaaaatgtttcttcat----tgttaagcaacaatgtggaac--attgattgtttcttgagctcgtggtgcgtgcttattttatcttggattcaatatgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACCGGGAGTCAGCTTAAGGAAGCTCAGAGCATTAACAAGTCATTATCAG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 22
--aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgttta--tttgtctttacatgacaattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
  ||  ||| |   ||| |    | ||      | | |    | | || || |  | |  || |    |||  |||| |      | |   | || || ||||||| ||||||||||||||||||||||||||||| ||||| || ||||| ||| | || | ||| |||||||||||||||||||| ||||||||| | ||||
ggaaaatgtttcttcattgt---taagcaacaatatggaacatcaattgtt-tcttgagcttgaggcatgtgcttacttattttatgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 22
------------------------------------------------------------------------aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgtttatttgtctttacatgacaattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
                                                                        | | ||||  ||  || |     || | | || | |      |   ||||   |    ||| ||    |||  |||     |||   | |     | ||| |||||||||||||||||||||| |||||||| || || || || ||||||||||||| ||||||||| ||||||||||| |||||||| ||| | ||||
gtattggtgtacattacttcaattttacctttgaatatcagtatgaatgttaatataccatattcttcctttattttgtggcaatttgaaacacaag-tattttat-gacctcgaggcattgcagt----ttttttaacttttttatgctggatttgtcatttgtcatacagTTAAGTTTTGTGGATCTTGCTGGCTCAGAAAGAGTAAAAAAGTCGGGCTCTTCAGGTAGTCAACTTAAAGAAGCTCAAAGTATCAACAAATCATTATCAG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 22
-------------------------------------------------------------aatctgtgttaac-atggagtg-tgagatgtcttgttggggcttacttattgtgataatgtttattt-gtctttacatgacaattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
                                                             | |||   || |  ||| ||   |  ||    |   |   |  |     | | |  |||||  ||||   ||||  |||     |||   | |     | ||| |||||||||||||||||||||| |||||||| || || || || || |||||||||| ||||||||| ||||||||||| |||||||| ||| | ||||
gtattattgtacattacttgtattttacctttgaatatcagtatgaatgttagtataccatattcttcctttattatgtagcaattcgaaacataagtattgtatgacc-tcgaggcaatgtggattttaactttttatgttggatttgtcatttgtcatacagTTAAGTTTTGTGGATCTTGCTGGCTCAGAAAGAGTAAAAAAGTCTGGTTCTTCAGGTAGTCAACTTAAAGAAGCTCAAAGTATCAACAAATCATTATCAG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgtttatttgtctttacatgac---aattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
 || | | |||        | ||   |   |||||    |    | |   |||| ||| |  | | |  |   ||      ||||||       ||| ||||||| ||||||||||||||||||||||| || || || || || || |||||  | |||  |||||| || ||||||||||| |||||||| |||||||| |
-atat-tattagtcaatgatatgccctccattgttaaacccatatcacc-tgatcatggtggtatcttctacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 3'ss of exon 23
aatctgtgttaacatggagtgtgagatgtcttg---ttggggcttacttattgtgataatgtttatttgtctttacatgacaattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
   |     |    ||   ||| || |   |     || |   |||   ||||   || |  ||  |    ||   |     |||||  |  ||| |  |||||| ||||||||||||||||| || || ||||| ||||||||||| || ||    ||| | ||||| || || || |||||||| || || ||  | ||||
---caagaatggtgtgccttgttagtttcgtcacattttgtaattagcaattgcactatttcttggtgaatttctgaattttattttggacttctctgagcagCTGAGTTTTGTGGATCTTGCGGGCTCTGAAAGAGTGAAGAAATCTGGATCCAGTGGTGAACAACTGAAAGAGGCCCAAAGCATTAATAAATCTTTGTCAG

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|30252243|gb|CB969794.1|CB969794
EST:     TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|71877730|gb|DT026785.1|DT026785
EST:     TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAG                         CTAATTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCACGCTCT
genomic: TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|71880280|gb|DT029335.1|DT029335
EST:     TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|110361383|gb|EC924851.1|EC924851
EST:     TGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|30252330|gb|CB969881.1|CB969881
EST:     TCAGTTGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
EST: gi|30252250|gb|CB969801.1|CB969801
EST:     TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAG                         CTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT
genomic: TTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatctt ... ctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtgataatgtttatttgtctttacatgacaattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
                                           ctctatct  CT-rich tract
                                 aattttaaaactctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgtttatttgtctttacatgacaattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - catggag
- - - - - - - - - - - - - - - - gttgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgac