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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgcagactctaaaaagtctgcttgcctacagccatttacaccttctggaaatggccttttacaaactagttataacttacgtacaattcaaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGTTTGGGGTTGTACAAGATGCTGATCGCCTTGATGCAATTGGTGCAATTG

Basic information

species Vitis vinifera
transcript Vv01s0011g02070.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g34470.1 (Oryza sativa), 3'ss of exon 4
aatgcagactctaaaaagtctgc-ttgcctacagccatttacaccttctggaaatggccttttacaaactagttataacttacgtacaattcaaattt------cagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGTTTGGGGTTGTACAAGATGCTGATCGCCTTGATGCAATTGGTGCAATTG
       | | | | ||   ||  |    |  || |  | |    ||||     |  || |    |  | |   |||  |||   |||  |||||| |      |||| |||||| | ||| || ||  |    ||  || |||   | |||  |||||||   ||||||||||||| ||||| ||||||||||||||||||||||
------cattatgataatgttgtatcatatgaaggccataagtagttcttagtgtatccctagttatgcaatgcatacgttata-acatctcaaatcttatgtgcagGATTCAAAAATGAAGTTTCAAAGAAGTCTGTTGTTGAGCCTACTCTTGAGTTTGCAATTGTACAAGATGCAGATCGTCTTGATGCAATTGGTGCAATTG

upper sequence: Vv01s0011g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G459291_T03 (Zea mays), 3'ss of exon 3
----aatgcagactctaaaaagtctgcttgcctacagccatttacaccttctggaaatggccttt-tacaaactagttataacttacgtacaattcaaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGTTTGGGGTTGTACAAGATGCTGATCGCCTTGATGCAATTGGTGCAATTG
     ||    |  || |   || |  |||  ||   | | | |  | |||| | |||     ||  | ||  |  || ||||   | |  |||  ||| | |||| |||||| | ||| || ||       ||| || |||     |||  || ||||   ||||||||||||| |||||| | ||||||||||| |||||||
catccataagtatgcttatt-gtataattgtttattcctagtgaatcattcttgcaattatgattgcaaaatgtccttctaacc--cctttaat--aaactgcagGGTTCAAAAATGAAGTTTCAAATAAATCTATTGTTGAGCCCACTCTTGAATTTGCAATTGTACAAGATGCAGATCGCTTGGATGCAATTGGGGCAATTG

upper sequence: Vv01s0011g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G02920.2 (Glycine max), 3'ss of exon 2
--aatgcagactctaaaaagtctgcttgcctacagccatttacaccttctggaaatggccttttacaaactagt-tataacttacgtacaa--ttcaaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGTTTGGGGTTGTACAAGATGCTGATCGCCTTGATGCAATTGGTGCAATTG
   |||    |||||||||||   ||||| |  | |  |||     ||    |  |   || |||| |   | |    || |||  | |    | |||  |||||||||||| || ||| |  ||||   ||  ||| |||||     |||||| ||||| ||||| |||||||||||||| |||||||| |||||||| || |
tgtatgtgtgctctaaaaagta-acttgcttctaccactttgtgaatt----actttttctattactagaaaatactcaatttagatgctgcttccaatgttcagGTTTCAAGGAAGAAGTGTCAGGAAGTGGAAATAGTGAAGGGTTTCCAGAATTTGGAGTTGTGCAAGATGCTGATCGACTTGATGCTATTGGTGCTATAG

upper sequence: Vv01s0011g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G17330.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------aatgcagactctaaaaagtctgcttgcctacagccatttacaccttctggaaatggccttttacaaactagttata-----acttacgtacaattcaaat--------ttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGTTTGGGGTTGTACAAGATGCTGATCGCCTTGATGCAATTGGTGCAATTG
                 | |    |||| || |  ||   |   ||| |   || ||||   | |   | |    ||     |    ||| ||     | ||  | |||   ||| |        | ||||||| ||||| ||| | |||||  | ||     |||| | || |||||| |||||||| || ||||||||||||||||||||||||||||| || || |
gtcagtttccagctcctactttttactc-aacatatccaatcaactata---atgtacatgatttatcactacaattaagtcattctgttgtatataaatttgtgaacagaacaagtgtattctttccagGTTTTAAAGACGAATTAGCAGGAGTAGCACTCTGTGAGTCTCTTCCAGAATTTGGGGTAGTTCAAGATGCTGATCGCCTTGATGCAATTGGCGCCATAG

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|110730534|gb|EE107722.1|EE107722
EST:     CATANAGGAGAGCAAGAGGATGAAAATATTAAGCATCATAAAGGCAATGG                         GTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGT
genomic: CATAGAGGAGAGCAAGAGGATGAAAATATTAAGCATCATAAAGGCAATGGgtaagtctct ... caaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGT
EST: gi|294965477|gb|GW839048.1|GW839048
EST:     CATAGAGGAGAGCAAGAGGATGAAAATATTAAGCATCATAAAGGCAATGG                         GTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGT
genomic: CATAGAGGAGAGCAAGAGGATGAAAATATTAAGCATCATAAAGGCAATGGgtaagtctct ... caaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGT
EST: gi|110415762|gb|EC981694.1|EC981694
EST:     CATAGAGGAGAGCAAGAGGATGAAAATATTAAGCATCATAAAGGCAATGG                         GTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGT
genomic: CATAGAGGAGAGCAAGAGGATGAAAATATTAAGCATCATAAAGGCAATGGgtaagtctct ... caaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGT
EST: gi|37190640|gb|CF609989.1|CF609989
EST:     CATAGAGGAGAGCAAGAGGATGAAAATATTAAGCATCATAAAGGCAATGG                         GTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGT
genomic: CATAGAGGAGAGCAAGAGGATGAAAATATTAAGCATCATAAAGGCAATGGgtaagtctct ... caaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggaaatggccttttacaaactagttataacttacgtacaattcaaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGTTTGGGGTTGTACAAGATGCTGATCGCCTTGATGCAATTGGTGCAATTG
                              aacttac  putative branch site (score: 2)
                                      tacaattcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgcagactctaaaaagtctgcttgcctacagccatttacaccttctggaaatggccttttacaaactagttataacttacgtacaattcaaatttcagGTTTCAAAGAGGAACTTGCAGGGTTTGCTAATGGTGAATATCCTCCAGAGTTTGGGGTTGTACAAGATGCTGATCGCCTTGATGCAATTGGTGCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
aatgcag
- - - - - - aaaaagt
- - - - - - - - - - - - -gcctaca
- - - - - - - - - - - - - - - - -ccattta
- - - - - - - - - - - - - - - - - - - - - - - - - -aatggcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaacta