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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag

Basic information

species Vitis vinifera
transcript Vv02s0025g02140.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 2
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag
|||| || || ||||| || || ||||||||||| ||||||||||| ||||| ||  | || ||||| ||||| ||||| ||  | || ||||||||||||||||  | |  | || |  | |||    |    |   |  | ||  |   ||  |     |   ||||    | |||| | | ||| |||
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTGAACCCAGAGAGGACCATCTTCGATGTCAAACGTCTCATTGGAAGAAAgtaat--ggcactttaccctatgctc---gctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttg-cag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 2
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggt-ctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag
|||| || || ||||| || || ||||||||||| ||||||||||| ||||||||  | || ||||| |||||||| || ||| | || || ||||||||||| | | ||| ||   | |  |||| |  |  |  |  | |   | | |         | | || |      |    ||  |||       
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCTGTCAACCCTGAGAGGACCATCTTTGACGTCAAGCGTCTCATCGGAAGAAAgtagtgcctctctcccacaattgcttctattatttcgtctcgctgtgggttatgtctggcgtcttacctgtaatgcccattgcttag-----

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 2
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatct---atctaaagcttttggtctatgcattgt-attagttggcaaggaactttttgctgaggcttttaatcacttttgacag
|||| || || ||||| || || ||||||||||| ||||||||||| || |||||  | || ||||| |||||||| || ||| | || || |||||||||||| || ||| ||    |  ||   || |||   |  |  | ||  |  |||      |   | ||  ||   |   |    || || |   ||
TCACCGATAGCGAGAGGCTCATCGGTGAGGCTGCCAAGAACCAGGCAGCCGTCAACCCTGAGAGGACCATCTTTGACGTCAAGCGTCTCATCGGAAGAAAgtaacacctctctcctacagttacttctgttgaatttcgtctcgttgtgggttatttctggcgtcttaactttagtaatgccccatttatt-tag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 2
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag
|||| |||||||||||||| ||||| |||||||| ||||| | ||| ||||||||| | |||||||| ||||||||||| ||||| |||||||||||||||||| || |        || ||| | ||| | | || |   | | | |||    |    |   || |||      |     |||||| |||
TCACCGACAGTGAGAGACTAATTGGAGAGGCTGCCAAGAATCTGGCAGCTGTCAATCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaagactta-------ctcaagttgttgatttttg-acaatttgatttgatggga---tcaatggtgactgacatgtatccttttg-cag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 2
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag
|||| |||||||||||||| ||||| |||||||| ||||| ||||| ||||||||  | |||||||| ||||||||||| ||||| ||||| |||||||||||| || |        || ||| | ||| | | || |   | | | ||||   || |    ||| |   |  ||  |||  ||||  |||
TCACCGACAGTGAGAGACTCATTGGGGAGGCTGCCAAGAATCAGGCAGCTGTCAACCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATCGGAAGAAAgtaagacttg-------ctcaagttgttgatttttg-acaatttgatttggt--gggatcaattgttactgacttgcatc--tttttgcag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 2
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag
|||| |||||||||||||| ||||| |||||||| ||||| | ||| ||||||||  | |||||||| ||||||||||| ||||| |||||||||||||||||| || |   || |  | |   |||||        |||  ||| | ||| |   |  |  |  ||||   || |     |||||  |||
TCACCGACAGTGAGAGACTAATTGGAGAGGCTGCCAAGAATCTGGCAGCTGTCAACCCAGAAAGGACCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaagacttac-tcaagttga--tttttgaca-----atttgatttgatgggatcaa--tggtgactgacatttat-----ctttttgcag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 2
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggtctatg--cattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag
|||| |||||||||||||| ||||| |||||||| ||||| | ||| ||||||||  | ||||||   ||||||||||| ||||| |||||||||||||||||| || ||       || ||| ||||| | || |   |||  ||| | ||  ||  ||  | |  ||||    | |     | |||  |||
TCACCGACAGTGAGAGACTCATTGGGGAGGCTGCCAAGAATCTGGCAGCTGTCAACCCAGAAAGGGTCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaagacatc-------ctcaagtttttgatttaggacaatttgatttgatgtgaataaaggtgt--ctgacatgtat-----ccttttgcag

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 2
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag
| ||||||  ||| || || |||||||||||||| ||||| ||||||||||| ||| | || |||||| |||| || || |||||  | || ||  |||||||||   |   ||| | |     ||||  |||||   ||   |  | ||  |  |    |||   |     || | ||    |||| |||
TTACTGACTCTGAAAGGCTCATTGGTGAGGCTGCTAAGAATCAGGCGGCTGTTAATCCTGAGAGGACTGTCTTCGACGTTAAGAGATTGATCGGGCGAAAgtaattacttattctcttt----tttttcttctatatgtt---tgtgatgatattgttggtttaattc---tttcttattgtatttggcag

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|161716815|gb|FC069176.1|FC069176
EST:     GCCGAAACGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAA                         GTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAAGAT
genomic: GCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtc ... cttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACAT
EST: gi|110725909|gb|EE102862.1|EE102862
EST:     GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAA                         GTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAAGAT
genomic: GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtc ... cttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACAT
EST: gi|352777237|gb|FQ473870.1|FQ473870
EST:     GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAA                         GTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACAT
genomic: GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtc ... cttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACAT
EST: gi|110685799|gb|EE062845.1|EE062845
EST:     GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAA                         GTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAAGAT
genomic: GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtc ... cttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACAT
EST: gi|110709376|gb|EE084780.1|EE084780
EST:     GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAA                         GTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAAGAT
genomic: GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtc ... cttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACAT
EST: gi|110703620|gb|EE080624.1|EE080624
EST:     GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAA                         GTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAAGAT
genomic: GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtc ... cttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACAT
EST: gi|33401982|gb|CF207609.1|CF207609
EST:     GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAA                         GTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAAGAT
genomic: GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtc ... cttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACAT
EST: gi|110687283|gb|EE064556.1|EE064556
EST:     GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAA                         GTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAAGAT
genomic: GTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtc ... cttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTGACAGTGAGAGACTGATTGGTGAGGCTGCGAAGAACCAGGCGGCTGTCAATGCCGAAAGGACTATCTTTGATGTGAAGAGGCTTATTGGAAGAAAgtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA