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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGAAGAGTTTTACCTAAACATGGTTTCAGAGCGACTTGGGAGTAGCATAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaaacataaattcattttttgttactattagtccatgaaagaccctttatgattgaaaccattgttctttacactcgtttattatctttctttattgccccttaatttatgacgggatctgttttttacag

Basic information

species Vitis vinifera
transcript Vv01s0127g00260.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA01G03530.1 (Glycine max), 5'ss of exon 4
CAATGAAGAGTTTTACCTAAACATGGTTTCAGAGCGACTTGGGAGTAGCATAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaaacataaatt-cattttttgttactattagtccatgaaagaccctttatgattgaaaccattgttctttacactcgtttattatctttctttattgccccttaatttatgacgggatctgttttttacag
|||||||||||||||||| ||||| || || ||| |||||||||  |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||   | |||||  || ||  |||       | ||||  ||   | |   | |     |||||   ||   | ||| |   ||| |  ||     ||  |    | | |                           
CAATGAAGAGTTTTACCTTAACATTGTCTCCGAGAGACTTGGGAACAGCATAAGCTTTTCAGAATGTGGAGGAATTGAAATTGAAGACAACTGGGATAAGgtactaaaatacatatttttcacctttcagattaaatagtttat---atattttgtgcatgtgaaa---tttccccttatatatgtt-acgatgcggtttattcatacttcag--------------------------

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G04120.2 (Glycine max), 5'ss of exon 4
CAATGAAGAGTTTTACCTAAACATGGTTTCAGAGCGACTTGGGAGTAGCATAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaaacataaattcattttttgttactattagtccatgaaagaccctttatgattgaaaccattgttctttacactcgtttattatctttctttattgccccttaatttatgacgggatctgttttttacag
|||||||||||||||||| ||||| || || ||| |||||||||  || ||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||   ||| | | |||  |    | | |   | | |   | | | |   |  |    |||||   ||   | ||| |   ||| |  || |   ||  |      | |                           
CAATGAAGAGTTTTACCTTAACATTGTCTCCGAGAGACTTGGGAACAGTATAAGCTTTTCAGAATGTGGAGGAATTGAAATTGAAGACAACTGGGATAAGgtacta--aaatacatatttttcacctttcagattaaataatttatatattttgcacatgtgaaa---tttccccttatatatgtt-acaatgtggtttgttcatatttcag--------------------------

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G17010.2 (Glycine max), 5'ss of exon 4
CAATGAAGAGTTTTACCTAAACATGGTTTCAGAGCGACTTGGGAGTAGCATAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaaacataaattcattttttgttactattagtccatgaaagaccctttatgattgaaaccattgttctttacactcgtttattatctttctttattgccccttaatttatgacgggatctgttttttacag
|||||| ||||||||||| ||||| || |||||| |||| |||| ||| ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||| |    |  ||||  ||      ||   | ||||| |  | | ||   |   |   | |     | | ||  ||  ||   | | |  |  | | ||  |      | |                           
CAATGAGGAGTTTTACCTTAACATTGTCTCAGAGAGACTAGGGAATAGTATAAGCTTTTCTGAATGTGGAGGAATTGAAATTGAGGAGAATTGGGATAAGgtgccaaaattcatactttttgaccttacaaatattacttgaagtaaattctgctcatact----tcctcgtaattcccataagct-acaaagtgttttgttcatatttcag--------------------------

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA15G42140.2 (Glycine max), 5'ss of exon 3
CAATGAAGAGTTTTACCTAAACATGGTTTCAGAGCGACTTGGGAGTAGCATAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaaacataaattcattttttgttactattagtccatgaaagaccctttatgattgaaaccattgttctttacactcgtttattatctttctttattgccccttaatttatgacgggatctgttttttacag
|||||| ||||||||||| ||||| || |||||| |||| ||||  || ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||| |  | |||   | | |  |||    | || | || |   |  |||     ||||| |   |     |  |  || |  |   |||  |  | | ||  |      | |                           
CAATGAGGAGTTTTACCTTAACATTGTCTCAGAGAGACTAGGGAACAGTATAAGCTTTTCTGAATGTGGAGGGATTGAAATTGAGGAGAATTGGGATAAGgtgc--caaaattcatactt-tttgacctcacaaataattacttgaag-taaattatgctcatatttcctcgtaattcccataagttacaaagtgttttgttcatatttcag--------------------------

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 5'ss of exon 5
CAATGAAGAGTTTTACCTAAACATGGTTTCAGAGCGACTTGGGAGTAGCATAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgta----cttctaaacataaattcattttttgttactattagtccatgaaagaccctttatgattgaaaccattgttctttacactcgtttattatctttctttattgccccttaatttatgacgggatctgtttttta--cag---------------------------
||  || || || ||||||   || || ||||| || |||||   ||  || ||||| ||||||||||||||||| ||||||||||| |||||||| || |||    ||  | |   |       || ||| ||   ||   |        |  |   | ||    | ||      | |      ||   |   |  ||| |||||| |      |  |     |    |||||| |||  ||                            
CAGCGACGAATTCTACCTATCTATTGTGTCAGATCGGCTTGGAGCTAATATCAGCTTCTCCGAATGTGGAGGTATAGAAATTGAAGAAAACTGGGAAAAAgtaagagctcatgactcttgtgctgttatttcttttcatagattggattggggacagatctggactagactggaagtttcattgttctacttccaagtttgtttatttctatgagaccttaccggccgcctgtttcttagccaatgttggactaatctggatggggttcag

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|294965404|gb|GW837119.1|GW837119
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGGGGCCCACTTT-ACCTCAGAAATTTG
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGGCC-ACTTTTACCTCAGAAATTTG
EST: gi|110730830|gb|EE108354.1|EE108354
EST:     TAAGCTTTTCTGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
EST: gi|294966134|gb|GW837501.1|GW837501
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAAACGGTGCCACTTT
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGGCCACTTT
EST: gi|71860189|gb|DT009244.1|DT009244
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGG
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGG
EST: gi|110731355|gb|EE105692.1|EE105692
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
EST: gi|110730143|gb|EE106883.1|EE106883
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
EST: gi|111125102|gb|EE253720.1|EE253720
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
EST: gi|294965669|gb|GW837268.1|GW837268
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGGGGGCCACTTTTACCTCAGAAATTTG
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGG-CCACTTTTACCTCAGAAATTTG
EST: gi|71863321|gb|DT012376.1|DT012376
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGGGGCCGCTTTTACCTCAGAAATTTGT
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
EST: gi|161718453|gb|FC065040.1|FC065040
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT
EST: gi|161714091|gb|FC064386.1|FC064386
EST:     TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAG                         GTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATATGT
genomic: TAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaa ... ttttttacagGTTAAAACTATATTTATCCCAACCGGGGCCACTTTTACCTCAGAAATTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATGAAGAGTTTTACCTAAACATGGTTTCAGAGCGACTTGGGAGTAGCATAAGCTTTTCCGAATGTGGAGGTATTGAAATTGAAGAGAACTGGGATAAGgtacttctaaacataaattcattttttgttactattagtccatgaaagaccctttatgattgaaaccattgttctttacactcgtttattatctttctttattgccccttaatttatgacgggatctgttttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA