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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttatgaacatccttctggatttcttgattcttttatcagtttcctcatttcttgtttttaattgactatattcgattttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT

Basic information

species Vitis vinifera
transcript Vv18s0001g14670.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
gtaatcttatgaacatccttctggatttcttgattcttttatcagtttcctcatttcttgtttttaattgactatattcgattttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT
|||||||  |   |     | |  | ||||  || |||      |||| ||  |  |  ||| |||| |   |   ||||   |   ||||| |||||||||||||| ||| | |||||  |||| ||||| || ||||| |||||  |||| || ||||| || || ||||||||||||||||| |||||
gtaatctggttg-cgctgctatctaattctgcatgctt------gttttcttctaccaagttattaagtttttcc-ttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT

upper sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 2
-------gtaatcttatgaacatccttctggatttcttgattcttttatcagtttcctcatttcttgttttt--aattgactatattcgattttga--------acagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT
       |  ||| |||     |   | ||    | ||    | ||| |   | ||||  || ||||||| |  || ||  |  | |  || ||           |||| || ||||||||||| ||| | |||||  |||||||||| || ||||| |||||| |||| || ||||| || || || |||||||||||||| |||||
gtgaccagctatcctattt-tgttactttgatgcttttcccccctttgtgcatatcctttttccttgtttatcaaaatggttgaacttcatctttgcaactgccgcagGTCAAGAGGATTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGT

upper sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 2
-----------------------gtaatcttatgaacatccttctggatttcttgattcttttat-cagtttcctcatttcttgttttt---aattgactatattcgattttg--------aacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT
                        |   ||  |    ||  | ||   ||| |   ||| |||   |  | ||||  ||  |||||  |   ||| |   |  ||| || ||         || ||| || ||||||||||| ||| | |||||  |||||||||| || ||||| |||||| |||| || ||||| || || || || ||||||||||| |||||
gtgactagccgtgctgttctgtcctgtcctgctacttatgatgctttttttttcctttcctttgcgcgatatcctttttctttgttcatcaaaatggttgagcttccatctttgcaactgtaatagGTCAAGAGGATTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAAGCCAGCTATGAGAATGT

upper sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 2
gtaatcttatgaacatccttctggatttcttgattcttttatcagtttcctcatttc--ttgtttttaat---tgactatattcgattttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT
||||  |    ||   |  |     | | | | ||    ||||| ||||  ||| |   |||||| | ||   | |  |||||   |  | |||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || || || ||||| || |||||||| |||||||| |||||||||||| |
gtaacatggcaaaa--caattcaattatatagttttcagtatcattttctgcatattgtttgtttctgatggtttaacatattgtttgattaacagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATGTCTTCATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATAT

upper sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G02540.2 (Glycine max), 3'ss of exon 2
gtaatcttatgaacatccttctggatttcttgattcttttatcagtttcctca--tttcttgtttttaattgactatattcgattttga---acagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT
|||||  |||||  | |  ||    | | | || |    |||   |||   ||  ||  ||||||||  | |  ||  |||   |||||   ||||| ||||| ||||| |||||  | |||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||||| |||||||||||| |
gtaat--tatgacaaccaatccacttatatagaattgggtattgtttttgacaaattgattgtttttggtggtttaacttcttgtttgattaacagGTCAGGAAGATTATAATAGGCTTAGACCCTTGAGCTATCGAGGAGCTGATGTTTTTATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATAT

upper sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G02580.2 (Glycine max), 3'ss of exon 2
gtaatcttatgaacatccttctggatttcttgattcttttatcagtttc--ctcatttcttgtttttaattgactatattcgattttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT
|||||  |||||  | |  |   | | | | || ||   ||| | |||   || |||  |||||| |  | |  ||  ||   |  | |||||| ||||||||||| |||||  | ||||||||||| |||||||| ||||| || ||||| ||||| || |||||||| |||||||| |||||||||||| |
gtaat--tatgacaaccaattcagttatatagaatcgggtattatttttgactaattgtttgtttctggtggtttaacttgtttgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATGTATTTATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATAT

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|46910991|gb|CN546366.1|CN546366
EST:     TGTGGTTGTTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTG                         GCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACG
genomic: TGTGGTTGTTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTGgtaatcttat ... ttttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACG
EST: gi|30299923|gb|CB976717.1|CB976717
EST:     TTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTG                         GCCACGATGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCAGACG
genomic: TTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTGgtaatcttat ... ttttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACG
EST: gi|30300001|gb|CB976795.1|CB976795
EST:     GTGGTTGTTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTG                         GCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCAGACG
genomic: GTGGTTGTTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTGgtaatcttat ... ttttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatcagtttcctcatttcttgtttttaattgactatattcgattttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT
                             aattgac  putative branch site (score: 3)
                     ttgtttttaattgact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttatgaacatccttctggatttcttgattcttttatcagtttcctcatttcttgtttttaattgactatattcgattttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG