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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagttacagtggcagttggtgttaattttcttttacatattacttgaaatgcagtttgtcttatcaataaatgtaactttcaactactcaatggaggtttttttcccaacag

Basic information

species Vitis vinifera
transcript Vv18s0001g09320.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 5
ATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgta-------------acagttacagtggcagttggtgttaattttcttttacatattacttgaaatgcagtttgtcttatcaataaatgtaactttcaactactcaatggaggtttttttcccaacag
|||||| || ||||||||| | || ||||| || |||   |||||||| ||||| || ||||||||||| || ||||||||||| ||||||||              |   ||| |     |     |   ||||  | |   | || | ||  ||||     ||| | |||  | | ||   |  |   |    | | |    ||||||    ||    
ATACTTCAAAGGGCCTGAATTGCTGGTTGACTTCCAAAGTTATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATGgtgtgtttgccctcctatgattataa-aataacctatcaaaattgccatggccttacttctgtaaatt--acttg-cgtatagaaagatagcaactgttatgctttatttactgtttttgatgcag---

upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA01G39950.1 (Glycine max), 5'ss of exon 5
ATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagttacagtggcagttggtgttaattttcttttacatattacttgaa---atgcagtttgtctta---tcaataaatgtaactttcaactactcaatggaggtttttttcccaacag------------
|||||||||||||||||||||||| ||||||||||||||||||||||| || || |||||||||||||| || || |||||||| ||||||||   | | | |    ||  |  |  | ||| | | |  |||| |  |   |   |||||| | |||| |   | |  | |  | | ||  || |     ||   |||  |  |    |  |            
ATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGATATGTGGAGCCTTGGCTGCATGTTTGCTGGAATGgtgtgaatcataactacaagt--ttctgattatatatggcatactcttgacatttatgcagatggtctaaatttgagcatacatga-ttaaaaatgtgagattctggtcataattttcattgtactttttgtag

upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA11G05340.2 (Glycine max), 5'ss of exon 5
ATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagttacagtggcagttggtgttaattttcttttacatattacttgaa---atgcagtttgtctta---------tcaataaatgtaactttcaactactcaatggaggtttttttcccaacag--------
|||||||||||||||||||||||| ||||||||||||||||||||||| || || || ||||||||||| || || |||||||| ||||||||   | ||| |     |  |  |  |  || | | |  |||| |  |   |   |||||| | |||| |         |  || | |  || | | || | ||      |  || ||      ||          
ATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATGgtgtgaattataactataagt--tactggttatatatggcatactcttgacatttatgcagatggtctaaatttgagcgtacatgattaaaaatgtaaaattctggtcataatttgttcgttgtactcttttgtag

upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G22250.1 (Glycine max), 5'ss of exon 5
ATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagttacagtggcagttgg-----tgttaattttcttttacat---------attacttgaaatgcagtttgtctt---atcaataaatgtaactttcaactactcaa----tggaggtttttttcccaacag
|||||||||||| ||||||||||| |||||||| |||||||||||||| || || || |||||||| || || || |||||||| |||||||| | | ||| ||    ||         |  |  || | | | ||||         |||| |||| ||| ||| |   ||   ||| | |  |  ||  |      | ||      ||    | ||  | |    ||
ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTCATTAGACATGTGGAGTCTTGGCTGCATGTTTGCTGGAATGgtgagaattatagctataggctacaacttactggttatatgtgacatgctcttggcattatttgatatgaagtctaattttgaatctacatgtacaaaatcgtgtaattctgggtttgatcatcttacttcatgtag

upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA17G17790.1 (Glycine max), 5'ss of exon 5
ATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagttacagtggcagttgg-----tgttaattttcttttacata---------ttacttgaaatgcagtttgtctt---atcaataaatgtaa--ctttcaactactcaatggaggtttttttcccaacag---
|||||||||||| ||||||||||| |||||||| |||||||||||||| || || || |||||||| || || || |||||||| |||||||| | | ||| ||    ||         |  |  || | | | |||||         ||| || | ||| ||| |   ||   ||| | |  |  ||     |  | | ||   |   | |  |||| |  |  |   
ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTCATTAGACATGTGGAGTCTTGGCTGCATGTTTGCTGGAATGgtgagaattatagctataggctacaacttactggttatatgtgacatacccttggcgttatttaatatgaagtctaattttgaatctacatgtacaaaatcgtgtaattctgggttatgatcattttacttaatgcag

upper sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 5'ss of exon 5
ATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagttacagtggcagttggtgttaattttcttttacatattacttgaaatgcagtttgtcttatcaataaat--gtaactttcaactactcaatggaggtttttttcccaacag---
 ||||||||||| || ||  | ||||| ||| | |||||||| || ||||||||||| ||||||||  |||| || |||||||| ||||||||||    |  | |     |   | || | |||    |  | ||| | ||||   ||  || ||  || ||| ||   | |  || |||   || |  ||      |||    ||  |   
GTACTTTAAGGGCCCAGAGTTACTTGTCGATCTTCAAGACTACGATTATTCTTTGGACATGTGGAGTTTAGGATGCATGTTTGCTGGAATGgtaaggaatgtatt----ctatattttgaattttgcatgtacatt-cctgaagccca--ttatcccat-aatgaaccagcaggttgcaaac-ctgacaggctaccatttgtttaattgtag

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|26265141|gb|CA816204.1|CA816204
EST:     ATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATG                         ATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTT
genomic: ATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagtta ... ttcccaacagATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTT
EST: gi|26267081|gb|CA818144.1|CA818144
EST:     ATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATG                         ATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTT
genomic: ATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagtta ... ttcccaacagATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTT
EST: gi|34549230|gb|CF517462.1|CF517462
EST:     ATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATG                         ATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTT
genomic: ATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagtta ... ttcccaacagATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATGgtaacagttacagtggcagttggtgttaattttcttttacatattacttgaaatgcagtttgtcttatcaataaatgtaactttcaactactcaatggaggtttttttcccaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG