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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttctttctctgtcttactatcaatagggcctaagcctatttgtagacaactcatggatgattgaacttcttgtaattattttcttgtaatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG

Basic information

species Vitis vinifera
transcript Vv13s0101g00090.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0101g00090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g44440.1 (Oryza sativa), 3'ss of exon 1
---tttcttctttctctgtcttactatcaatagggcctaagcctat--ttgtagacaactcatggatgattgaacttcttgtaattattttcttgtaatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG
|| | || | || | | | || || | | | || || | || | | || || | ||| || | | |||| | ||||||| || ||||||||||| |||||||| || ||||||||||| || || ||||| || || ||||| ||||||||||||||||| ||||
tgcattgtagcttacgagcttttttgtta-tatgggttgaacatacaattattagaaaagctcagtaaatctaaatactt----ttctccttttgttccttgcagAATTCAAATGGGATGATGTTAAGGTTGACAAGCACCGAGAGAATTACCTCGGTCATAGCATTAAGGCTCCTGTTGGAAGATGGCAGAAAG

upper sequence: Vv13s0101g00090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G12330.1 (Glycine max), 3'ss of exon 1
tttcttctttctctgtcttactatcaatagggcctaagcctatt-tgtagacaactcatggatgattgaacttcttgtaattatttt-cttgtaatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG
|| || |||| | || | | | || ||| | | | | ||| ||||| | |||| | |||| || | ||| |||||||| | ||||| ||||| || | |||||| || | ||||||||||||||||||||||||||||| ||||||||||||||||| ||||
--tcacaaacttcatgcttaggagtaaaaaaactcatgcatataattttaattatctatgtatgatattgatgtttgtttgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG

upper sequence: Vv13s0101g00090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G06270.1 (Glycine max), 3'ss of exon 1
tttcttctttctctgtcttactatcaatagggcctaagcctatttgtagacaactc-----atggatgattgaacttcttgtaattatttt-cttgtaatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG
|||| | || | |||| || |||||| | |||| || ||| ||| | || | | |||| || | ||| |||||||| | ||||| ||||| || |||||||| || | ||||||||||||||||||||||||||||| || |||||||||||||| ||||
----gattttcacaaaattcatgct--taggagtaaaaaacttttgtatataacttcaatgatttatgtatgatatcgatgaacgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG

upper sequence: Vv13s0101g00090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G52220.1 (Arabidopsis thaliana), 3'ss of exon 1
-----tttcttctttctctgtcttactatcaatagggcctaagcctatttgtagacaactcatggatgattgaacttcttgtaattattttcttgtaatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG
|| || | || || ||||| | || | || | | || | | | | || | || | | ||||| ||||||| | |||||||| ||||||| ||||||| | | ||||||||| | |||||||||||||| |||||||||||||||||||||||||
agatcgtttttggcaattagttttcaaatcaaagatgtagaacatgagctgctaatgat-----gagaactctattactaattgaatttgtttataaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGGGTCACAGTATCAAAGCCCCTGTTGGAAGATGGCAAAAAG

upper sequence: Vv13s0101g00090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S59_322V6.1 (Physcomitrella patens), 3'ss of exon 1
tttcttctttctctgtcttactatcaatagg-gcctaagcctatttgtagacaactcatggatgattgaacttcttgtaattatttt--cttgtaatgtc--cagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG
|||| || | | || | | ||| | || | || | || | || | ||| ||| ||| || | | || | |||| ||||| |||||||||||||||| || || ||||| ||||| || ||||||||||| ||||||| |||||||| ||||||| || |
----aattttcaatgggatgcaattatgggacattcaaggtcctctggacgtaaatgatatgaggc-gactgtgttgacattttttaaactgggattggctgcagAGTTTAATTGGGATGATGTCAAGGCCGACAAGCACCGCGAGAATTACCTTGGTCACAGCCTCAAGGCTCCTGTTGGGCGATGGCAGAAGG

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|161707046|gb|FC055923.1|FC055923
EST:     CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATC                         AATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
genomic: CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATCgtaaacgctc ... taatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
EST: gi|294965987|gb|GW839326.1|GW839326
EST:     CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATC                         AATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
genomic: CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATCgtaaacgctc ... taatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
EST: gi|26262262|gb|CA813325.1|CA813325
EST:     CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATC                         AATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
genomic: CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATCgtaaacgctc ... taatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
EST: gi|110413752|gb|EC979558.1|EC979558
EST:     CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATC                         AATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
genomic: CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATCgtaaacgctc ... taatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
EST: gi|161705888|gb|FC055363.1|FC055363
EST:     CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATC                         AATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
genomic: CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATCgtaaacgctc ... taatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
EST: gi|26267163|gb|CA818226.1|CA818226
EST:     CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATC                         AATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
genomic: CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATCgtaaacgctc ... taatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
EST: gi|26265069|gb|CA816132.1|CA816132
EST:     CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATC                         AATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
genomic: CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATCgtaaacgctc ... taatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
EST: gi|71871170|gb|DT020225.1|DT020225
EST:     CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATC                         AATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG
genomic: CTGGAAAATGTATCATCCTACCAGAGGTGGCGTTCGCGGTGGACGAGATCgtaaacgctc ... taatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagacaactcatggatgattgaacttcttgtaattattttcttgtaatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG
                                     ttttcttgt  CT-rich tract
 ttgtaattattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttctttctctgtcttactatcaatagggcctaagcctatttgtagacaactcatggatgattgaacttcttgtaattattttcttgtaatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - ctatcaa
- - - - - - - - - - - - - - - - -ctaagcc
- - - - - - - - - - - - - - - - - - - - - - - - - caactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcttg