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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCTGCTGCATCAAATCTGGGAAAGTTTGCTGCTACTGTTGAAGCTGCTCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggattttgtaatatgtatgcgtatttgattccactctttgattgctatgatatgcatacacacttttctatttgagttatttgttcaattttct...

Basic information

species Vitis vinifera
transcript Vv17s0000g03870.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G122135_T04 (Zea mays), 5'ss of exon 3
AGATCTGCTGCATCAAATCTGGGAAAGTTTGCTGCTACTGTTGAAGCTGCTCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggattttgtaatatgtatg---cgtatttgattccactctttgattgctatgatatgcatacacacttttctatttgagttatttgttcaattttct
||| |||||||||||||||| ||||||||||| || || ||||||     |||||||||| | || || |||||||||||||| ||  | || || |||||||  |    | |  | | |  |||    || ||   || |    |||| |   |      ||||    ||    ||   |   |||   |||     ||   
AGAGCTGCTGCATCAAATCTTGGAAAGTTTGCAGCCACAGTTGAACAGAATCATTTGAAGACAGAAATAATGTCAATATTTGATGACTTAACCCAAGATGgtacattttctatacagtttcaatgaactgtgttgtgttgcttcatttgttatttggttcctgcagttgcaggaatcatctcttgttccctgtctttctt---

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 3
AGATCTGCTGCATCAAATCTGGGAAAGTTTGCTGCTACTGTTGAAGCTGCTCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggattttgtaatatgtatg---cgtatttgattccactctttgattgctatgatatgcatacacacttttctatttgagttatttgttcaattttct---
||| | || ||||||||||| ||||||||||| ||||| ||||||     |||||||||| | || || |||||||||||||| ||| | || || |||||||  |    | |  | | |  |||    || ||   |||| |  |||| ||  |      ||||   |   ||  ||      ||||||||| |  ||||     
AGAGCAGCAGCATCAAATCTTGGAAAGTTTGCAGCTACAGTTGAACAGAATCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattctatatacagtttcaatgaaatgtgttgtgttcctccgtttgtttcttgcttcttgcactgattattccct------gttatttgtcctttttttcgag

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G10000.1 (Glycine max), 5'ss of exon 2
AGATCTGCTGCATCAAATCTGGGAAAGTTTGCTGCTACTGTTGAAGCTGCTCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggattttgtaatatgtatgcgtatttgattccactctttgattgctatgatatgcatacacacttttctatttgagttatt-tgttcaattttct-
||||| |||||  |||| |||||||||||||| || |||||||||||| |||| |||||  |||||||||||||  | ||||||||||| ||||||||||||||||| | ||| |   ||         |      || |    ||| | || | | ||  |||      |   |     |||| || |||     ||||| 
AGATCCGCTGCCACAAACCTGGGAAAGTTTGCCGCAACTGTTGAAGCTCCTCACTTGAAATCTGACATCATGTCTGTGTTTGAGGATCTCACACAGGATGgtatgtgaagtttatgtgataccactaattccagcaccgcatcatgaat-ctgttaaata-atagtaggataaatgcaacagtttttgtgtctgtatttcta

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA09G31760.1 (Glycine max), 5'ss of exon 3
AGATCTGCTGCATCAAATCTGGGAAAGTTTGCTGCTACTGTTGAAGCTGCTCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggattttgtaatatgtatgcgtatttgattccactctttga--ttgct--atgatatgcatacacacttttctatttgagttatttgttcaattttct
|||||||| ||  ||||  ||||||||||||| ||||||||||||||| |||| |||||  |||||||||||||  | ||||||||||| ||||| ||||||||||| | ||  |   ||         |  |   || |   ||||   || |  || |||     | | |     |  |||| |||  |  ||   ||||  
AGATCTGCGGCCACAAACTTGGGAAAGTTTGCCGCTACTGTTGAAGCTCCTCACTTGAAATCTGACATCATGTCTGTGTTTGAGGATCTCACACATGATGgtatgtgaagttgatgtgataccactaattccggcaccgcatcttgaatctgttaaataatagtaggataaatgcaacagtttgtgtttgtaatt--gtttt--

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|110723764|gb|EE101450.1|EE101450
EST:     CATTTGAAAGCTGACATCATGTNCA-TATTTGAGGATCTGACACAGGATG                         ATCAAGATTCTGTTAAGTTATTGGCTGTTGAGGGTTGTGCAGCTCT
genomic: CATTTGAAGGCTGACATCATGT-CAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCT
EST: gi|110698010|gb|EE075532.1|EE075532
EST:     TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATG                         ATCCAGATTCTGGTAGGTTATTGGCTGTTGAAGGTTGTGCANCTCTCGGAA
genomic: TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAA
EST: gi|352778272|gb|FQ465582.1|FQ465582
EST:     TCATTTGAAGGCTGACATCATGTCAATATCTGAGGATCTGACACAGGATG                         ATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAG
genomic: TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAG
EST: gi|352763901|gb|FQ465351.1|FQ465351
EST:     TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATG                         ATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGGA
genomic: TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAA
EST: gi|352776769|gb|FQ472656.1|FQ472656
EST:     CATTTTGA-GGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATG                         ATCAAGATTCTGT
genomic: CATTT-GAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGT
EST: gi|352773443|gb|FQ472225.1|FQ472225
EST:     TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAAGATG                         ATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAACTCTCGGAA
genomic: TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAA
EST: gi|156738161|gb|EV242282.1|EV242282
EST:     TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATG                         ATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAA
genomic: TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAA
EST: gi|110696169|gb|EE075018.1|EE075018
EST:     TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATG                         ATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAA
genomic: TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAA
EST: gi|30302057|gb|CB978851.1|CB978851
EST:     TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATG                         ATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAA
genomic: TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAA
EST: gi|352772524|gb|FQ471999.1|FQ471999
EST:     TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATG                         ATCAAGATTCTGTTAGGTTA
genomic: TCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggat ... ttcatttcagATCAAGATTCTGTTAGGTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCTGCTGCATCAAATCTGGGAAAGTTTGCTGCTACTGTTGAAGCTGCTCATTTGAAGGCTGACATCATGTCAATATTTGAGGATCTGACACAGGATGgtatgtggattttgtaatatgtatgcgtatttgattccactctttgattgctatgatatgcatacacacttttctatttgagttatttgttcaattttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG