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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct...

Basic information

species Vitis vinifera
transcript Vv13s0067g01290.t01
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 5
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatatt-aggaat--tttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct
||||||||| | ||||||||| | || || || || | |||||||| ||||| ||||| ||||| ||| | ||||||||||| ||||| ||||||||||| | | || || || | | | | || | | || |||| | || || | ||| | | |||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttacttctgtccatatctgacggtgatgtttgtttatgtataatttactatggtaacatccatgctgcgtgtgcag----------------------

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 26
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgt-cattctcatatattaggaattttaggagggaaatta-gcttgcgactttcccagcctgtgggccttttttagagct
||||||||| | ||||||||| | || || ||||| | |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||||||||| | | | |||| || ||| | | | | | | | || | | | | | | || | | || || | || | | |
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgt-acgtagtaatttctgtccatgttcgtgccgacgtct----atttacatacagtttaccatagtaacatctctactgtgctatgtgactgtgtgcgcag-

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct
||||||||| | ||||||||| | || || || || | |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||| ||||| | | | |||| || ||| || | | | || | | | | | | | | || || | || | | |
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgt-acgtagtaatttctgtccatgt---tcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag-

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G115138_T01 (Zea mays), 5'ss of exon 12
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgt-cattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct
||||||||| | ||||||||| | || || || || | |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||| ||||| | | | |||| || ||| | | | | | | | | || | | || | | | | | || || | || | | |
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgt-acgtagtaatttctgtccatgttcgtgccgacgtctatttacatacagttaccatagtaacat----ccctactgtgctatgtgactgtgtgcgcag-

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 5
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaatta-gcttgcgactttcccagcctgtgggccttttttagagct
|||||||| | ||||||||| | || || || || | |||||||| ||||| ||||| || || ||||| ||||||||||| || || ||||||||||| | || |||| ||| | | | || || | || | | | || | | || | ||| |||| | |
CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaacttatttctgcccgtacctgtggtg-atgtttgt--ttacatatagtttactatggtaataacat--ccatcctgcgtgtgcag---------

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct
||||||||| | ||||||||| | || || || || | |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||| ||||| || || ||| | || | | | | | || | | | | | | || | || | |||| ||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtct----atttacatacagtttacca--tagtaacatccctactatgtgcgcag-----------

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct
||||||||| | ||||||||| | || || || || | |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||| ||||| | | | |||| || ||| | || | | | || | | | | | | | | || || | || | | |
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgt-acgtagtaatttctgtccatgttcgtgtcg-acgtct--atttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag-

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 27
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct----------------------------
|| || ||||| ||||| || || || || ||||||||||||||||| | |||||||| ||||||||| ||||||||||||| |||||||| ||||||| | || ||||| || | | | | || ||| || || |||| | | | | | ||||||| | |
-TGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTTTGCCTTCCCATATCTCCTGCAGGt--ttgtattccttctgtgctgcttacttttattacttaaacatacatcgacatgtattatttctttttcaacattttatctagtgcttttttttaattaattgtcttcttctttcgctgatgtagt

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 28
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtg---atctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct
|| || ||||| ||||| || | || || ||||||||| ||||||||| || ||||| |||||||| ||||||||||||| |||||||| |||||||| || ||||| | || | | | || | | || | |||||||| | | | || || | | ||| | | | | | | | |
ATGTCTATTTGTTTGCTATGATCTCATACGGGCAGACATTGTTCTTGAACTAGCTTGGATGCACAATATGATTGACTTTGCCTTCCCATATCTATTGCAGgtttgcatttgttttatgctgctaatttgtatcacctgtagttagaattttatgtttcatgattcaatgtgattcagctagc-tattgatttgtatcataa--

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 27
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct-------------------
|| || ||||| ||||| || || || || |||||||||||||||| | |||||||| ||||||||| ||||||||||||| |||||||| ||||||| | || ||||| || | | | || ||| || || || || | | | ||| | ||| | ||
GTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAGTTGGCCTGGATGAACAATATGATTGACTTTGCCTTCCCATATCTCCTGCAGgt--ttgtattccttctgtgctgcttacctttattacttaaacatacatcgacatgtatgtctttttcatcatgttatgtagtgcgttctttcactatcttcttttttcgctgttgtag

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttc--------ccttgtcattctc------atatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct
|| |||||||| || || |||||||| || |||||| | ||||| |||||||||||||| ||||||||| | ||||||||||| || ||||| | |||||||||| | | || ||| | |||||| || | |||| | | | || || | | ||||| | ||| || |
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag-

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 28
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctc------atatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttt-tttagagct
|| |||||||| || || |||||||| || |||||| ||||||| |||||||| ||||| ||||||||| | ||||||||||| || ||||| | ||||| || | | | | || | ||| || |||||| || | || | | || | | || || ||| || | ||
ATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACTTTGCCTTCCCGTATCTCCTCCAGgtaatttatcctccaatccctaaaataccctctacctgatgagataggaaccatactgacgctatga--tcaactctctttgatcccgtcattttttcttcacag--

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|71858842|gb|DT007897.1|DT007897
EST:     TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAG                         TTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTG
genomic: TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtt ... tttctttcagTTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTG
EST: gi|161720108|gb|FC066740.1|FC066740
EST:     TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAG                         TTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG
genomic: TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtt ... tttctttcagTTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG
EST: gi|30128782|gb|CB914121.1|CB914121
EST:     TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAG                         TTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG
genomic: TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtt ... tttctttcagTTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG
EST: gi|30136332|gb|CB921670.1|CB921670
EST:     TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAG                         TTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG
genomic: TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtt ... tttctttcagTTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG
EST: gi|294964474|gb|GW838277.1|GW838277
EST:     TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAG                         TTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG
genomic: TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtt ... tttctttcagTTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG
EST: gi|33402568|gb|CF208195.1|CF208195
EST:     TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAG                         TTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG
genomic: TTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtt ... tttctttcagTTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttccc