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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttgcattgtttaacactttttatggttattgtcatctttccccttcatatactaatttccatttagctaagaatgtgcccctggacactttctgtttagtttaaaataaagtcattttgtcctaaattcttctggtatgttttgggtttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACTGGAGAGGCAGTTCTCCGGAAATGCTGAATCTCGAGCTGCTGGCATGGTG

Basic information

species Vitis vinifera
transcript Vv14s0066g02630.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G038588_T03 (Zea mays), 3'ss of exon 4
gtaacttgcattgtttaacactttttatggttattgtcatctttccccttcatatactaatttccatttagctaagaatgtgcccctggacactttctgtttagtttaaaataaagtcattttgtcctaaattcttctggtatgttttgggtttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACTGGAGAGGCAGTTCTCCGGAAATGCTGAATCTCGAGCTGCTGGCATGGTG-----------------------
                                          | || || ||     | |||       || | |     | |  || |   || ||||  |    |    |    |   |    | |     | |    | |   ||| |||       ||| | ||||  ||  | |||||||| ||| |||||||||| |||  |||| ||||||  |||||||| || |||||||||||| | || || || |||||                        
-----------------------------------------gtacctctccac---tttattctttggcagttga-----tactacttggtgctgtctgcattaactctgttcttttgtctactgctttggcaccttaactgtcgcttgtgtt-accaacagtattaatgcggatgtttacaaagTTCTTATGAAGGAGCTAGCTAAAACATTGGAGAAACAGTTCTCTGGCAATGCTGAATCTAGGGCAGCAGGAATGGTTATCAATACAATGGGGTGGGTTGA

upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G038588_T02 (Zea mays), 3'ss of exon 4
gtaacttgcattgtttaacactttttatggttattgtcatctttccccttcatatactaatttccatttagctaagaatgtgcccctggacactttctgtttagtttaaaataaagtcattttgtcctaaattcttctggtatgttttgggtttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACTGGAGAGGCAGTTCTCCGGAAATGCTGAATCTCGAGCTGCTGGCATGGTG
                                          | || || ||     | |||       || | |     | |  || |   || ||||  |    |    |    |   |    | |     | |    | |   ||| |||       ||| | ||||  ||  | |||||||| ||| |||||||||| |||  |||| ||||||  |||||||| || |||||||||||| | || || || ||||| 
-----------------------------------------gtacctctccac---tttattctttggcagttga-----tactacttggtgctgtctgcattaactctgttcttttgtctactgctttggcaccttaactgtcgcttgtgtt-accaacagTATTAATGCGGATGTTTACAAAGTTCTTATGAAGGAGCTAGCTAAAACATTGGAGAAACAGTTCTCTGGCAATGCTGAATCTAGGGCAGCAGGAATGGTT
















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|351053969|gb|FQ441735.1|FQ441735
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|351048068|gb|FQ441240.1|FQ441240
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|351037774|gb|FQ464215.1|FQ464215
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTCGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|22013971|gb|BQ799005.1|BQ799005
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|352791526|gb|FQ481105.1|FQ481105
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|351044652|gb|FQ443183.1|FQ443183
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|351053260|gb|FQ459128.1|FQ459128
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|161715992|gb|FC068763.1|FC068763
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|110422874|gb|EC989207.1|EC989207
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|352789973|gb|FQ479583.1|FQ479583
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|351046157|gb|FQ442535.1|FQ442535
EST:     ATTCCTCCTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|351037634|gb|FQ462618.1|FQ462618
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|351039234|gb|FQ457909.1|FQ457909
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|351042381|gb|FQ442848.1|FQ442848
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|351056907|gb|FQ443534.1|FQ443534
EST:     ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
EST: gi|110731309|gb|EE105610.1|EE105610
EST:     ATCCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAG                         TGCCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT
genomic: ATTCCTCTTGAAATGCCTCTTGTTTATTTCTATGGCCACACAACTCCTAGgtaacttgca ... ttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaataaagtcattttgtcctaaattcttctggtatgttttgggtttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACTGGAGAGGCAGTTCTCCGGAAATGCTGAATCTCGAGCTGCTGGCATGGTG
                 tcctaaa  putative branch site (score: 2)
                    taaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttgcattgtttaacactttttatggttattgtcatctttccccttcatatactaatttccatttagctaagaatgtgcccctggacactttctgtttagtttaaaataaagtcattttgtcctaaattcttctggtatgttttgggtttggtgttagTGTCAATGTAGAGTTATACAAAGTGCTTGTGAAGGAGCTTGCTCGAACACTGGAGAGGCAGTTCTCCGGAAATGCTGAATCTCGAGCTGCTGGCATGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT