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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgatttttccaatgcaaaaatgttacttaggaaaatcggttttgtgttggttttagtaatttgcatgaagacaattcgcatttttttttggtggga...

Basic information

species Vitis vinifera
transcript Vv06s0004g05560.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 5'ss of exon 2
TTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgatttttccaatgcaaaaatgttacttaggaaaatcggttttgtgttggttttagtaatttgc--atgaagacaatt-cgcatttttttttggtggga
|  | || | |    | || || || |  ||||| ||||| |||||| |||| || ||||||||||||||||| ||||||||||| || || |   | ||||    || ||||||        |  | || |    |    |   |           || |    | |   |    ||  ||  ||| ||   | | ||  | 
TCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTACTCCAGgta--aatctttccaccttttccacatgacatcctcattcagtcctcacaccacccctaatcccatactagtcctaactcttatgcagttggatctagtttg-

upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G059282_T01 (Zea mays), 5'ss of exon 2
TTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgatttttccaatgcaaaaatgttacttaggaaaatcggttttgtgttggttttagtaatttgcatgaagacaattcgcatttttttttggtggga--
|  | || | |   || || || |||   ||||| |||||   ||||| ||| || ||||||||||||||||||||||| ||||| || || |   | ||||||  ||  || |  | ||     |  | |    |   ||  |    | |  |  ||  | |  || | ||  | |   ||| | ||  |||   |     
TCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgcttactttccactttcgacaatcgtcatcttctttcccctttcaggctt--tcacctgtaagacaatagcccgcttgttacttttaggcagcc

upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G41410.1 (Glycine max), 5'ss of exon 2
TTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgatttttccaatgcaaaaatgttacttaggaaaatcggttttgtgttggttttagtaatttgcat-gaagacaattcgcatttttttttgg-tggga-
| || || ||| | || || ||||| || || || ||||| |||||||||||||| |||||||| |||||||| || || |||  ||| ||||| || ||||| |  ||| |||         || | ||  |     ||   |    ||||   ||| ||  ||  | | ||   | ||| |  ||| |  |||  |  || 
TCGCTGAGAGGCAGCACGGCGAAGTTACCTTTCCTGAGATCAGCACCACCATTCTCGAGAAGATTTGCCAGTACTTTTATTGGCATCTCCAATTCGCCAGgtttttctttctccctcttcgctat-tcacacattgccat--atacgatgttatctttcgtttttcactttgacagctatttgtttttgtaattgaatatgaa

upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA15G03990.2 (Glycine max), 5'ss of exon 2
TTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgatttttccaa-tgcaaaaatgttacttaggaaaat-cggttttgtgttggttttagtaatttgcatgaagacaattcgcatttttttttgg-tggga---
| || || ||| | || || ||||| || || || ||||| |||||||||||||| |||||||| |||||||| || || |||  ||| ||||| || ||||| |  ||| |||   | |   | |   || | |  | || ||   || | ||   |||   | ||||  ||    | |||    ||| |  |||  |  ||   
TCGCTGAGAGGCAGCACGGCGAAGTTACCTTTCCTGAGATCAGCACCACCATTCTCGAGAAGATTTGCCAGTACTTTTATTGGCATCTCCAATTCGCCAGgtttttctttctccctcttcgctattcgcacattgccatatacgacattatctttcgttt--cactttgactg----ctatttatttttgtaattgaatatgaatg

upper sequence: Vv06s0004g05560.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT5G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
TTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgatttttccaatgcaaaaatgttacttaggaaaatcggttttgtgttggttt-tagtaatttgcatgaagacaattcgcatttttttttggtggga----------
|  |||||  | || |||| | ||| |||||||| || ||||||||||| || || |||||||| |||||||| |||||||||||||||||||   | ||||||    || || ||          |  |||   |      | | |   ||| | | ||| |  | ||||      | |     ||  ||||     | |          
TCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttcca--ttatctaac---------tcgcttttcacctcttgctctacattgatctctagaacatggcattgtagtagtctctgttagttttcttcagaatcgcatcgct

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|77578280|gb|DV217915.1|DV217915
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|34319622|gb|CF372376.1|CF372376
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|32457151|gb|CD798325.1|CD798325
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAATCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|30326539|gb|CD009801.1|CD009801
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|32456769|gb|CD797943.1|CD797943
EST:     TCTCTCCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: TCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|77582862|gb|DV220412.1|DV220412
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|30134710|gb|CB920048.1|CB920048
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|110401168|gb|EC967768.1|EC967768
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|110421660|gb|EC987960.1|EC987960
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|30330192|gb|CD013454.1|CD013454
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|110413425|gb|EC979210.1|EC979210
EST:     GAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: GAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|22015221|gb|BQ800255.1|BQ800255
EST:     TCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: TCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|110418444|gb|EC984601.1|EC984601
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|32271968|gb|CD721127.1|CD721127
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|110408935|gb|EC974583.1|EC974583
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|77578008|gb|DV217766.1|DV217766
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|110392803|gb|EC957238.1|EC957238
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|110371311|gb|EC935227.1|EC935227
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|71861463|gb|DT010518.1|DT010518
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|110701302|gb|EE078715.1|EE078715
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
EST: gi|22010533|gb|BQ795567.1|BQ795567
EST:     ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAG                         TGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT
genomic: ATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgattt ... ccattgccagTGGGAAGGATACTGAGTTTCCGATTGAACCTGAGCTTACTCTGGAGCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgatttttccaatgcaaaaatgttacttaggaaaatcggttttgtgttggttttagtaatttgcatgaagacaattcgcatttttttttggtggga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagacaa