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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtatgtgtctgtgcacataggagagtgtgataagagggagggagggagggactctatgcctattcatgttctctttacttcaatgcacaccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGGATGGTTTTTTGGTTGGTGGAGCTTCCTTAAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g04800.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G04290.2 (Glycine max), 3'ss of exon 6
-----------tgtatgtgtctgtgca-cataggagagtgtg--ataagagg--gagggagggagggactctatgcctattcatgttc--tctttacttcaatgca-----caccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGGATGGTTTTTTGGTTGGTGGAGCTTCCTTAAAG
| | | | || | ||| | | | ||| ||| | | | | | || ||| || |||| | | | | | ||||| | || || |||||||||||||||||||| |||||||||||||||| | | || | ||||| ||||| |||||||||||||| || ||| | |||
gtaatcttgcatccaatttaccctgtatcattgtataatgtatcatatgtagtttacttgagttgtatgtcaatgaataaacatggtaagtttcttatccaatgaagcattcattaactgcagGTTCTGTAAATGGAGGAAACTGCAAAGAATTGGCCGCACAGCCCGATGTTGATGGATTTTTGGTTGGTGGTGCCTCCCTGAAG
















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|110415564|gb|EC981483.1|EC981483
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|110390656|gb|EC955578.1|EC955578
EST:     TAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|351028511|gb|FQ444792.1|FQ444792
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|110389346|gb|EC954175.1|EC954175
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|22015534|gb|BQ800568.1|BQ800568
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|34551021|gb|CF519221.1|CF519221
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|33409412|gb|CF215039.1|CF215039
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|51989908|gb|CV179363.1|CV179363
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGTCAACGCAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|110378426|gb|EC943557.1|EC943557
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|110692722|gb|EE068329.1|EE068329
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGT
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGT
EST: gi|110395870|gb|EC961544.1|EC961544
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|349826936|gb|FQ419027.1|FQ419027
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|110404715|gb|EC970203.1|EC970203
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|32461078|gb|CD802252.1|CD802252
EST:     TGATAATGCGGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|161714171|gb|FC062916.1|FC062916
EST:     TGATAATGCTGGAGATGA-GTTGCTGC-TCAACTAGAAT-ATTTACGGAG                         GT-CTGTAA-TGGAGCAA-CTGCAA-GAAT-GACA-CGCA-CTAGATGTG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTG
EST: gi|110364963|gb|EC928597.1|EC928597
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|110411583|gb|EC977303.1|EC977303
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG
EST: gi|33409496|gb|CF215123.1|CF215123
EST:     TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAG                         GTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACACAACTAGATGTGG
genomic: TGATAATGCTGGAGATGAAGTTGCTGCATCAACTAGAATTATTTACGGAGgtatcatcct ... ccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagggactctatgcctattcatgttctctttacttcaatgcacaccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGGATGGTTTTTTGGTTGGTGGAGCTTCCTTAAAG
                tattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatgtgtctgtgcacataggagagtgtgataagagggagggagggagggactctatgcctattcatgttctctttacttcaatgcacaccaattgcagGTTCTGTAAATGGAGCAAACTGCAAAGAATTGACAACGCAACTAGATGTGGATGGTTTTTTGGTTGGTGGAGCTTCCTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
-gtatgtg
- - - - - - -gcacata
- - - - - - - - - - - - - - -gataaga
- - - - - - - - - - - - - - - - - - gggaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcac