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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgcagatcccttctctacccttgcttcacagcatttgttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT

Basic information

species Vitis vinifera
transcript Vv10s0071g01150.t01
intron # 1
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
--tctgcagatcccttctctacccttgcttcacagcatttgttattttga-attttgaatttttacttct----cgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
  |||| ||     |  |  |    || |  |     || |||||   |  |  |||   |  ||  | |    |      || |||||||   |   || |   |||||| ||||| || ||  | |||| ||| ||||| |||||||||||||||||| | ||  |||||||||||||||| ||||| ||||| ||||| |||||
tgtctgaag-----tggtacattgatg-taaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgact-tgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT

upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 1
-tctgcag-atcccttctctacccttgcttcacagcattt--gttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
 |||| ||     | |   | |   |  |      |||    |    || |  | || ||||   ||   | |    ||| |||||||   |  ||| |   |||||| ||||| || ||||| |||| ||| ||||| |||||||||||||||||| | ||  ||||||||||||| || ||||| || || ||||| |||||
gtctgaagtggtacattgatgcaaataatatcagtcatcgagggagattgggctgttaaattcgcacacattgg---aatgccttgact-tgcatttggtgtagAGGAGTTTGTGGCGCACTCGTCCAATGTTAACTGCCTCAAGATTGGGAGGAAGACCTCGCGGGTTCTTGTCACAGGAGGAGAGGACCATAAGGTCAATCT

upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------tctgcagatcccttctctacccttgcttcacagcatttgttattttg-----aattttgaatttttacttct-----cgagaaaattccttgacc---acggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
                                                  | ||||    || |   |   ||  || || | |  |   || ||||     |  || || | |||  || |      | |  | ||   || ||   |||  || ||  |||||||||||||||||||  |||| | ||| || || |||||||||||  |||| |||||||||||||||||||| || || |||||||||||||| |||||
gtatccttcatctcttgtctgtctgtgctttacattttgtttgatctatctatgcactcgcccttcattttctatctgcagatctctctctactttgttattatgttagagtctttctttgtgtgtgtgtgtgacttggctggccttgacgagttatgtccagAGGAATTTGTAGCACATGCTTCTACTGTCAATTGCCTCAAGATTGGACGGAAATCATCCAGGGTTCTTGTCACTGGAGGTGAAGATCACAAGGTCAATCT

upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 2
----------------------------------------------tctgcagatcccttctctacccttgcttcacagcatttgttattttgaattttgaatttttacttctcgagaaaattccttgacc---acggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
                                              | ||||  | || ||  |   ||  || || | |  |   | | |     | |   | | |     | | |    |  |||| ||   |||  || ||  |||||||||||||||||||  |||| |  || || || |||||||||||  |||| |||||||||||||||||||| || || |||||||||||||| |||||
gtatccttcatctcttgtttgtctgtgctttacattttgtttgatctatgcacttgccctccattttctatctgcagatctctctctctctctctctctctctctctctacttggtgtgtgtgacttggccttgacgagttatgtccagAGGAATTTGTAGCACATGCTTCTACCGTCAATTGCCTCAAGATTGGACGGAAATCATCCAGGGTTCTTGTCACTGGAGGTGAAGATCACAAGGTCAATCT

upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 2
tctgcagatcccttctctacccttgcttcacagcatttgttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
| |||   |   ||    | | ||   |||     ||  ||   | || | |            |  |       |  |||          ||| |  |||||||||||| ||||| ||| |   ||| || ||||| ||||||||||||||||| ||||||||||| || || || ||||||||||||||||| |||||
tgtgcttctaaatttataaacttttagtcaatttcttctttgactagagtctcatcccagagtattgcttagccttgacttatgtgatacattttataagAGGAATTTGTGGCACATTCTGCTGCTGTTAATTGTCTTAAGATTGGGAGGAAGTCCTCCAGGGTTCTCGTTACAGGCGGAGAAGATCACAAGGTTAATCT

upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 2
-tctgcagatcccttctctacccttgcttcacagcatttgttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
 |      |   ||  | |        |  |       | ||   | || | |  |  |  ||| | | |   |   |       |   ||  || || |||||||||||| ||||| ||| |   ||| || ||||| ||||| || |||||||| || |||||||| || || ||||| |||||||||||||| |||||
ttaaatttaagactattatgaatgaagtcaagtttgagttttgactagagtctctatctggtacctattgcttagccttgactttctgtgtggtttaa-agAGGAATTTGTGGCACATTCTGCTGCTGTCAATTGTCTTAAGATCGGAAGGAAGTCTTCTAGGGTTCTGGTAACAGGTGGTGAAGATCACAAGGTCAATCT

upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S101_210V6.1 (Physcomitrella patens), 3'ss of exon 1
---tctgcagatcccttctctaccc-ttgcttcacagcatttgttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
     |     ||    | || |   ||| |        |  ||  || |   |   ||  || ||    |||    | | ||||||| ||     ||   ||||||| ||||| ||||||||||||| ||| ||||| ||||||||||||| |||||| || |||||  | |||||||| ||||| |||||||| || ||  |
aatcttattagtctaaacactccaaattgttgagtcatttacgtgcttattggtgaggatattgtataattcggtttagt-ccttgactactaccctt---cagAGGAGTTTGTTGCACACTCTTCCAATGTCAACTGCCTCAAGATTGGGAAGAAGTCCTCTAGGGTCTTGGTCACCGGCGGAGAGGATCACAAAGTCAACAT

upper sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ26184 (Selaginella moellendorffii), 3'ss of exon 1
tctgcagatcccttctctacccttgcttcacagcatttgttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaa---cagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
                                   |  |||  || | |||  |     ||   | ||       ||  |||| |  | |  | | |   ||||||| ||||| || || ||||||   || || || |||||||| ||||||||  ||||  |||| || |||||||||||||| ||||||||||| ||| |
----------------------------------gtgagtttcttcgcattcgg-----ttttctttcagagctgttggttgatcttgttggtggcaatccagAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCTCGTCACCGGTGGAGACGATCACAAGGTCAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT
                              ttccttgac  putative branch site 
                                            ttttt  putative PPT
     tttgaatttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgcagatcccttctctacccttgcttcacagcatttgttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
tctgcag
- - - - - ccttctc
- - - - - - - - - -cccttgc
- - - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaat