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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatattctattaacaatttttgtacttcatgtatattgtctgatttctttcacatacaataaatgtaatagttcttagagttttttctttcttttttttttttttttaaaaaaagggttcgattgaagcactttgtggacttgtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCCAAGCAGAAGAAAAAGAAGTCAAAGTCTAAGGTCTGCTCCATATTGTGAA

Basic information

species Vitis vinifera
transcript Vv04s0023g03860.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 6
gtttatattctattaacaatttttgtacttcatgtatattgtctgatttctttcacatacaataaatgtaatagttcttagagttttttctttcttttttttttttttttaaaaaaagggttcgattgaagcactttgtggacttgtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCCAAGCAGAAGAAAAAGAAGT-CAAAGTCTA--AGGTCTGCTCCATATTGTGAA
                                                                  | || || ||    |  |||  | ||||||||       |  ||||   ||  | | |    ||     |  | ||| | || ||||||||| | |||||||| ||||||   ||||| || ||||| || |||||||| ||||| ||||||||||||   ||||   |  |||  || || |||||||   
-----------------------------------------------------------------gtata-taattaaatgtatttcctttttcttttcacacaatggttaagttaattggtagtcataaatttatatttgaccttta-ttgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT---

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 7
gtttatattctattaacaatttttgtacttcatgtatattgtctgatttctttcacatacaataaatgtaatagttcttagagttttttctttcttttttttttttttttaaaaaaagggttcgattgaagcactttgtggacttgtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCCAAGCAGAAGAAAAAGAAGT-CAAAGTCTA--AGGTCTGCTCCATATTGTGAA
                                                                 |  |  | |     |    |||| |||| ||    |     |  | ||   |   |    || ||    |||| ||  |  | |||||||||  | |||||||| ||||||   ||||| || ||||| || |||||||| ||||||||||||||||||   ||||   |  ||| ||| || |||||||   
---------------------------------------------------------------gtacatggttgaatgcatttcttttacttttttaaaatcacaatggttaattcaatatgttgtttaatttttttggggggtatttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCCTGTTCGATATTGT---

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 7
gtttatattctattaacaatttttgtacttcatgtatattgtctgatttctttcacatacaataaatgtaatagttcttagagttttttctttcttttttttttttttttaaaaaaagggt--tcgattgaagcactttgtg----gacttgta---attgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCCAAGCAGAAGAAAAAGAAGT-CAAAGTCTA--AGGTCTGCTCCATATTGTGAA
                                                                              || |   ||   | | ||| |||| |||||||||||  | | |  |  ||| ||    |||        | | |||   ||| |||||  | |||||||| ||||||   ||||| || ||||| || |||||||| ||||||||||||||||||   ||||   |  |||  ||||| |||||||   
-----------------------------------------------------------------------------gtacatggttgaatgtatttcttttatttttttaaaatcacgatggttaattcaatgtttttaaaaaaaaattggtatttattacagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCATGCTCGATATTGT---

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|110376013|gb|EC941052.1|EC941052
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTATTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
EST: gi|110713128|gb|EE088780.1|EE088780
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTGTTTGATCAGGCCATTANGGTTGTGCTCCAACCACCC
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
EST: gi|110390015|gb|EC954898.1|EC954898
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTATTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
EST: gi|46918251|gb|CN547580.1|CN547580
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
EST: gi|110396036|gb|EC961711.1|EC961711
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTATTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
EST: gi|87586594|gb|DY474807.1|DY474807
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTATTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
EST: gi|110404309|gb|EC969170.1|EC969170
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTATTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
EST: gi|33410493|gb|CF216120.1|CF216120
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTATTTGATCAGGCCA
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCA
EST: gi|110366542|gb|EC930452.1|EC930452
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTATTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
EST: gi|110386939|gb|EC951574.1|EC951574
EST:     GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAG                         AATATCAAGGCAGTATTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC
genomic: GGCTGATTGATGCCCCTGCTTACATAGAATGCAGTGCCAAAACACAGCAGgtttatattc ... gtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttaaaaaaagggttcgattgaagcactttgtggacttgtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCCAAGCAGAAGAAAAAGAAGTCAAAGTCTAAGGTCTGCTCCATATTGTGAA
     tttttaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttatattctattaacaatttttgtacttcatgtatattgtctgatttctttcacatacaataaatgtaatagttcttagagttttttctttcttttttttttttttttaaaaaaagggttcgattgaagcactttgtggacttgtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCCAAGCAGAAGAAAAAGAAGTCAAAGTCTAAGGTCTGCTCCATATTGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT