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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA

Basic information

species Vitis vinifera
transcript Vv14s0060g01680.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
gtatgt-ctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
|||  | || || |||    ||    |  | | |||||      |||    |   ||||  || ||| | | |||||  | |||| ||||||||||||||| |||| || || || ||||||||  |||| || || |||||||||||||| |||||||| || |||||||| ||||| ||||
gtaaatgctcaatatcttttttggataaatacttcaaa------attcaggaaatttta--attatgcttccttcat--gcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
------------------gtatgtctaaaca--tcacagttttgcatct-tcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
                    |||  || | |   || |   | |  | | | |||      || |    | ||||  |   || |||   | |||  ||| |||| ||||||||||||||| ||||||| || || ||||| ||  |||| || || ||||||||||||||||||||||| ||||||||||| ||||| ||||
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggcctta-atcatgcatccttc--ttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
gtatgtctaaacatcacagttttgcatcttcatcaaattt--ggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
         ||  ||  | | ||  ||  | || ||||||   |  ||  | | | ||||  || |||   | |||||  | ||||  |||||||||||||| | || || || || ||||| ||  |||| || || |||||||| |||||||||||||| ||||||||||| ||||| ||||
-------gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagattta--atcatgcatccttcat--gcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
--gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagca-tgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
    ||||| | | ||   |||    |   | |||    ||  ||   |    |   |    | | ||| |   ||   |   |||||||||||||||||||| |||| |||||||| || ||||| || || ||||| |||||||| || |||||||||||||| || ||||||||||| || |
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
--gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
    ||||| | | || |||    ||    | |||  |     ||| |    |  || ||    | | |   ||  ||    |||||||||||||||||||| |||| || || || || ||||| ||||| ||||| |||||||| ||||||||||||||||| || ||||||||||| || |
gtacatgtccagagat-acaaccatgacattccatacagcc--gcaatgtttactgtatacttaggtttattttctatc---agGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 21
--gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
  || ||||  || || |||  | ||    | |||         ||||||  | | ||    || |  || ||||  ||| ||||||||||||||||||||| | || || |||||||| ||||||||||| |||||||| || || || ||||| || ||||| || ||||||||||| ||||
gtgtgtgtccgaatat-acaactctgatattccatt--------catttgttaagtttattgattactttactttt-tttatagGTAATGACAACATTCATGCCGCCGCCTCCTGCTTCTACCTTCCTAGCTTTCCATCCCCAGGATAACAACATTATTGCCATTGGGATGGAGGATTCAACCA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 21
--gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
  || ||||   | || |||  | ||    | |||         ||||||  | | ||    ||||  || ||||  ||| ||||||||||||||||||||| |||| || |||||||| ||||||||||| |||||||| || || || ||||| || ||||| || ||||| ||||| ||||
gtgtgtgtccggatat-acaactctgatattccatt--------catttgttaagtttattgatgactttactttt-tttatagGTAATGACAACATTCATGCCACCGCCTCCTGCTTCTACCTTCCTAGCTTTCCATCCCCAGGATAACAACATTATTGCCATTGGGATGGACGATTCAACCA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 20
------------------------------------gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttag----catgatgttgctttca--tttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
                                      || |||||     |  ||| | ||   | ||| | |      |||    || | ||     ||  |     || |     || ||||| ||||||||||||||| | ||||| || || ||||| ||  | || ||||||||||| ||||||||| |||| ||||| |||||||| || ||||| |
gtatatattatctatatgaacttaaaaaaagccacaagatttctaactgaaaatgttct-cacactaatctagtaaactcttttggttgttctaatttccacaaaaaaactattggccttatagGTGATGACAACATTCATGCCGCCTCCACCAGCATCAACGTTTTTGGCGTTCCATCCTCAGGACAATAACGTCATCGCCATTGGAATGGAAGACTCTACGA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
gtatgtctaaacatcacag---ttttgcatcttcatcaaatttggcatttga-aatggtttagcatgat----------gttgctttcat-ttgt-----agGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
 ||| |  ||| ||   ||   ||||  ||  | |  |||||   |   ||   ||| || | ||||            ||||| |||   ||||     |||| ||||| ||||||||| | || || || ||  | || || || || |||||||| |||||||| |||||||| |||||||||||||||||||| || |
-tat-taaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtgattcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
                       | ||   |||    |||  | | |  |  ||| ||    ||  ||||   ||| |  |||| |||||| |||||||| |||| || || ||  |||| ||||| || || || ||||||||||| || |||||||| || |||||||| |||||||| |
-----------------------gtatgcacat----ttttccttcttgaccggtgtaa---gaacttgc---catgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

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|71855117|gb|DT004172.1|DT004172
EST:     TGTCGGCCTGTGGTGGAAAAGTTTCCCTCTTCAACATGATGACATTCAAG                         GTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTC
genomic: TGTCGGCCTGTGGTGGAAAAGTTTCCCTCTTCAACATGATGACATTCAAGgtatgtctaa ... tcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
                                          ctttcattt  CT-rich tract
                atttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT