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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAATTTGTTGATAGATCGCCGTACTAATTCACTGAAGCTTGCAGATTTTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgctaccttatatgagcttctctagtcattgatgcagataataaaattgaaatggattggctttttcacaagaaaatgatatgccattatgct...

Basic information

species Glycine max
transcript GLYMA09G03470.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 4
ACAGAATTTGTTGATAGATCGCCGTACTAATTCACTGAAGCTTGCAGATTTTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgt---------ttgtgtgctaccttatatgagcttctctagtca---ttgatgcagataataaaattgaaatgg-attggctttttc---acaagaaaatgatatgccattatgct-----------------------
 |||||||| ||||||||||| ||||||||| |||||||||||||||| ||||| || || ||||||||||| ||||||||| | || ||||| ||||||||         |||||| | || || | |   ||||   |   |   ||  |     | ||||| || |  |   |||  | |||||   |||  |  |   ||   ||  |||                         
TCAGAATTTATTGATAGATCGGCGTACTAATACACTGAAGCTTGCAGACTTTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACATTTACTCATGAGgtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcag

upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 5'ss of exon 3
ACAGAATTTGTTGATAGATCGCCGTACTAATTCACTGAAGCTTGCAGATTTTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgt---------ttgtgtgctaccttatatgagcttc-tctagt-cattgatgcagataataaaattgaaatgg-attggctttttc---acaagaaaatgatatgccattatgct-----------------------
 |||||||| ||||||||||| ||||||||| |||||||||||||||| ||||| || || ||||||||||| ||||||||| | || ||||| || |||||         |||||| | || || | |   |||| |  ||| ||||  |     | ||||| || |  |   |||  | |||||   |||  |  |   ||   ||  |||                         
TCAGAATTTATTGATAGATCGGCGTACTAATGCACTGAAGCTTGCAGACTTTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactatagatttgtgttcaacattttgttttcttcataaagtacattttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcag

upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g03060.1 (Oryza sativa), 5'ss of exon 3
ACAGAATTTGTTGATAGATCGCCGTACTAATTCACTGAAGCTTGCAGATTTTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgt-gctaccttatatgagcttctctagtcattgatgcagataataaaattgaaatggattggctttttcacaagaaaatga-tatgccattatgct---
 |||||  || |||||||||| ||||| || ||| ||||||| || || ||||| ||||| ||||||||||||||||||||| |||| ||||| || |||||   | |  |  ||  | | |   |||  | |  |    ||    | |||    |    || |        | || ||||     | | |   ||  ||     
CCAGAACCTGCTGATAGATCGGCGTACCAACTCATTGAAGCTCGCGGACTTTGGGTTGGCCAGGGCATTTGGCATTCCTGTCCGGACATTTACTCACGAGgtacattttacagcccgacacgtttttcgtttggtac-actgtgatttatagtcct----tgcacatcacactacagaagaggggaactgtctaatggtgaaaac

upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 4
ACAGAATTTGTTGATAGATCGCCGTACTAATTCACTGAAGCTTGCAGATTTTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgctaccttatatga-gcttctctagtcattgatgcagataataaaattgaaatggattggctttttcacaag-----aaaatgat--atgccattatgct------------------------------------------------------------------------------
 ||||| |||||||||||||| |||| |||| |||||||||||||||| ||||| || || ||||||||||| ||||||||| | || ||||| ||||||||   | |||||   |   |   ||||  || |  |  |        ||| |   |   | |||     | ||      |     ||||| ||  || |||      |                                                                              
TCAGAACTTGTTGATAGATCGGCGTAATAATGCACTGAAGCTTGCAGACTTTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGTACATTTACTCATGAGgtaaatttgctatgctgcttattgcttaacttgagaaagggagtttgaattatcctattagggaaaaaatattgtgaggggtgccaaaattatggatcccaccgattttatacccatataacataaccttttgttgtctattctagtcatatcaactcaatacatatctatggaagtatttttcag

upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 4
ACAGAATTTGTTGATAGATCGCCGTACTAATTCACTGAAGCTTGCAGATTTTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgt-------ttgtgtgctaccttatatgagcttctct-agtcat--tgatgcagataataaaattgaaatggat----------tggcttt------ttcacaagaaaatgatatgccattatgct-----------------------------------------------------
 || || || ||||||||||| || |||||| |||||||||||||||| ||||| || || ||||||||||| ||||||||| | || ||||| ||||||||       || ||  ||| |||     ||    ||| | |  |  || |   || || || ||||  | ||||          ||| ||       ||   |    ||| |  |  | || ||||                                                     
TCAAAACTTATTGATAGATCGGCGCACTAATGCACTGAAGCTTGCAGACTTTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGTACATTTACTCATGAGgtacatttgttatgctctaacttgagaaagggagtctgaattgtcctgttagggaaaaaaatattgtgagggatgccaaagttatggattcccacaatttttacccgaataacgtaaccttttgctgtatattctagtcacattaattcacagtacatatctatggaagtatttttcag

upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 5'ss of exon 5
ACAGAATTTGTTGATAGATCGCCGTACTAATTCACTGAAGCTTGCAGATTTTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgctaccttatatgagcttctctagtcattgatgcagataataaaat--tgaaatggattggctttttcacaagaa-aatg---atatgccattatgct--
||||||||||||||| |||||||| || || |||||||||||||| ||||||||| |||| || ||||| || || ||||||||||| ||||| ||||||||          | ||||       ||  |  ||||   | |   | || ||||  |      |  ||  ||  | |  ||   ||||   ||     ||||| |   
ACAGAATTTGTTGATTGATCGCCGCACAAACTCACTGAAGCTTGCTGATTTTGGACTGGCCAGAGCATTCGGTATCCCTGTCAGGACATTTACTCATGAGgtac-caaagagctttat-------tccttgttcatatgttcccgttatgaaatcttttggctggctgcattccttatgagtgtaatgtaaattaagtattataccac

upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 5'ss of exon 5
ACAGAATTTGTTGATAGATCGCCGTACTAATTCACTGAAGCTTGCAGATTTTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgttt--gtgtgctaccttatatgagcttctctagtcattgatgcagataataaaattgaaatggattggctttttcacaagaaaatgatatgccattatgct--
 ||||| ||  | |||||||| ||||| ||| || | ||||| ||||| ||||||||||| || |||||||| |||||||| ||||| |||||||||||||| |   ||||| | |   | ||| ||  || |  ||| |||        |  | |||  ||        ||  | | |    | |   ||  || | |  |  
CCAGAACTTACTCATAGATCGTCGTACCAATGCATTAAAGCTGGCAGACTTTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgtgcaatcc-gtgtgacctcttcca--cat-gatttttcctctttacttggtatttgcatctttaataatatttgattatcatatcaattttttgc

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|120532704|gb|EH260837.1|EH260837
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192309059|gb|FK001835.1|FK001835
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192312501|gb|FK004987.1|FK004987
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|193726875|gb|FK661573.1|FK661573
EST:     TGGATTGGCTTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TGGATTGGC-TAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|151396909|gb|EV266782.1|EV266782
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192295604|gb|FG988178.1|FG988178
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|6073117|gb|AW102504.1|AW102504
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192330928|gb|FK023101.1|FK023101
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCG
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCG
EST: gi|9204181|gb|BE330405.1|BE330405
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192312081|gb|FK003858.1|FK003858
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|24136151|gb|BU926661.1|BU926661
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCCGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|151394972|gb|EV264843.1|EV264843
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGTTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|151409597|gb|EV279405.1|EV279405
EST:     TTGGGTTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCCCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192309058|gb|FK001834.1|FK001834
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192312486|gb|FK004986.1|FK004986
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|15813934|gb|BI786209.1|BI786209
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGG
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGG
EST: gi|193328289|gb|FK294310.1|FK294310
EST:     TGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
EST: gi|192300023|gb|FG991841.1|FG991841
EST:     TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAG                         GTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT
genomic: TTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgc ... ttgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGAATTTGTTGATAGATCGCCGTACTAATTCACTGAAGCTTGCAGATTTTGGATTGGCTAGGGCATTTGGCATTCCTGTCAGGACCTTTACACATGAGgtttgtgtgctaccttatatgagcttctctagtcattgatgcagataataaaattgaaatggattggctttttcacaagaaaatgatatgccattatgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatga