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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccaacattatttgcctattttttcggtctattaacatgggtcattttgggtatattactttttgttatatatgttatatatgctcgttaacattagtttctctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATAACTGATATGTGGGAGCCACTAGAAGAAGGCCTTCTTCC

Basic information

species Vitis vinifera
transcript Vv18s0072g00330.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00330.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g34940.1 (Oryza sativa), 3'ss of exon 2
gtaaccaacattatttgcctattttttcggtctattaacatgggtcattttgggtatattactttttgttatatatgttatatatgctcgttaacattagtttctctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATAACTGATATGTGGGAGCCACTAGAAGAAGGCCTTCTTCC
             |     |    || |    | | | ||  | | || ||||  ||||  ||   |||||   || |   || ||||  |  ||    |     |     ||||||||||||| ||||||||||||||| || || ||||  || |  || |||||||| |  ||||| ||| | |||||||| |||    |
------------gtaaatttgcaattccataatgtaatca--gataatattgg--atatccctcactgttacg-atatgccatgtgctgatctac----gccctccctgagcagAGAAGGATTGTTGGTCTCCATCAGAATACCTCTATTGAATCAATCGACATAACTGACACTTGGGAACCATTGGAAGAAGGGCTTAACAC

upper sequence: Vv18s0072g00330.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G142111_T01 (Zea mays), 3'ss of exon 2
gtaaccaacattatttgcctattttttcggtctattaacatgggtcattttgg-gtatattactttttgttatatatgtta--tatatgctcgttaacattagtttctctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATAACTGATATGTGGGAGCCACTAGAAGAAGGCCTTCTTCC
                            ||  |  ||| | |   ||| ||   | ||  |||  |||||  | ||||  |  |||   ||| |  | ||   | | ||     ||||||||||||||||||||||||||||| || || ||||  || | ||||||||| || |  ||||||||| | |||||||||||| |  |
--------------------------gtggaatgctaa-acgccacatgttaatgaatgataccctttgtagt-tatgccaattattgactcatatatat-gctatatcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC
















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|71875822|gb|DT024877.1|DT024877
EST:     CCATGGGCAGAGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAG                         AGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
genomic: CCATGGGCAGGGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAGgtaaccaaca ... tctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
EST: gi|349832332|gb|FQ420893.1|FQ420893
EST:     CCATGGGCAGGGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAG                         AGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
genomic: CCATGGGCAGGGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAGgtaaccaaca ... tctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
EST: gi|110379018|gb|EC944186.1|EC944186
EST:     CCATGGGCAGAGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAG                         AGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
genomic: CCATGGGCAGGGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAGgtaaccaaca ... tctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
EST: gi|71867579|gb|DT016634.1|DT016634
EST:     CCATGGGCAGAGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAG                         AGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
genomic: CCATGGGCAGGGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAGgtaaccaaca ... tctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
EST: gi|349811194|gb|FQ406182.1|FQ406182
EST:     CCATGGGCAGGGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAG                         AGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
genomic: CCATGGGCAGGGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAGgtaaccaaca ... tctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
EST: gi|349826958|gb|FQ419049.1|FQ419049
EST:     CCATGGGCAGGGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAG                         AGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA
genomic: CCATGGGCAGGGCAATCAACAAAACTGTGATGATTGCTGAACTAATTAAGgtaaccaaca ... tctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttttgttatatatgttatatatgctcgttaacattagtttctctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATAACTGATATGTGGGAGCCACTAGAAGAAGGCCTTCTTCC
                             cgttaac  putative branch site (score: 3)
                                         tttctctcattc  putative PPT
     tttgttatatatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccaacattatttgcctattttttcggtctattaacatgggtcattttgggtatattactttttgttatatatgttatatatgctcgttaacattagtttctctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATAACTGATATGTGGGAGCCACTAGAAGAAGGCCTTCTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG