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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttttttcgtagaggaaactctcacacctgttttggttttttaattgttaatttgtag

Basic information

species Glycine max
transcript GLYMA05G21370.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G899149_T01 (Zea mays), 5'ss of exon 3
GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttttttcgtagaggaaactctcacacctgttttggttttttaattgttaatttgtag
|| ||||| |||||| ||||  | ||||||||||||||||| |||||||| || |||||||||||||| ||||||||  ||||  ||| |    || | ||||  |    | |  | |  |||  |||    |||| |   ||      |  |||  |    | || |||  |     |   
GATAAGGCTATCAAGCGGTTCTTGGTGAGGAACATTGTTGAGCAGGCTGCCGTGAGAGATGTGCAGGAGGCCTGTGTACATGATGgtactgtagatatccttatttcttgcatgatttaatttaatttaactgtag-gttgaccagagaaattgtcctaacatgttcatt--tggacag---

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G899149_T02 (Zea mays), 5'ss of exon 2
---------------GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttttttcgtagaggaaactctcacacctgttttggttttttaattgttaatttgtag
               || ||||| |||||| ||||  | ||||||||||||||||| |||||||| || |||||||||||||| ||||||||  ||||  ||| |    || | ||||  |    | |  | |  |||  |||    |||| |   ||      |  |||  |    | || |||  |     |   
TTGCTGTACTTGCAGGATAAGGCTATCAAGCGGTTCTTGGTGAGGAACATTGTTGAGCAGGCTGCCGTGAGAGATGTGCAGGAGGCCTGTGTACATGATGgtactgtagatatccttatttcttgcatgatttaatttaatttaactgtag-gttgaccagagaaattgtcctaacatgttcatt--tggacag---

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G827266_T03 (Zea mays), 5'ss of exon 3
GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttttttcgtagaggaaactctcacacctgttttggttttttaattgttaatttgtag-----
|||||||| |||||||||||||  ||||||||||| || |||||||| ||  |||| || || |||||||| || ||||||||  |||| |||   | | || |  |     |  |  |||  |  |   || |  | | |||         ||    || |       |  ||      ||     
GACAAGGCGATCAAGAGGTTTCAGGTGAGGAACATCGTGGAACAGGCGGCCATCAGGGACGTCCAGGAAGCATGCGTCTATGATGGTAA-Aatctctctattcctctagatctgtttcgttagtaataaatctttaatgcaacctgttgttttgacgagggtaaacgtgttctatggctcaggctac

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G827266_T02 (Zea mays), 5'ss of exon 3
GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttttttcgtagaggaaactctcacacctgttttggttttttaattgttaatttgtag
|||||||| |||||||||||||  ||||||||||| || |||||||| ||  |||| || || |||||||| || ||||||||  |||| |||   | | || |  |     |  |  |||  |  |   || |  | | |||         ||    || |       |  ||      ||
GACAAGGCGATCAAGAGGTTTCAGGTGAGGAACATCGTGGAACAGGCGGCCATCAGGGACGTCCAGGAAGCATGCGTCTATGATGgtaa-aatctctctattcctctagatctgtttcgttagtaataaatctttaatgcaacctgttgttttgacgagggtaaacgtgttctatggctcag

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G129015_T02 (Zea mays), 5'ss of exon 3
GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttttttcgtagaggaaactctcacacctgttttggttttttaattgttaatttgtag
|| ||||| |||||| ||||  | ||||||||||||||||| |||||||| || || || |||||||| ||||||||  ||||  ||| | ||| |  || |  |||  |   |   |    |  | | ||  |||   |       | |||    ||  | | || |||   |        
GATAAGGCTATCAAGCGGTTCTTGGTGAGGAACATTGTTGAGCAGGCTGCTGTGAGGGACGTGCAGGAGGCCTGTGTGCATGATGgta-tcatagtcgtcct-tattagctgcatagtccgatgatctatttataggttatctagagaaaccgtccttaatatcttcatttgcacag-----

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G40510.1 (Arabidopsis thaliana), 5'ss of exon 3
GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttt----tttcgtagaggaaactctcacacctg----ttttggttttttaattgtt--aatttgtag----------------------------------------------------------
||||||||||| ||||||||  |||||||||||||||| || ||||||||  | |||||||| ||||||||  | ||||||||  |||  | |   || ||  | || |  || || ||   ||| ||    ||    |    ||| | |      |     | ||||| ||   |  |||   |||| | |                                                          
GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCTATTAGAGATGTTCAGGAAGCTAGCGTCTATGAGGgtatcatttcattcctctcttttatgtttctttgacctttgttataattctacattataaagtttggatttttagactattggtattgagaaagtttggatttttcgactattggcattgaagtttactgagatctgtaacttgattgaatcatgtaattgacag

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G40590.1 (Arabidopsis thaliana), 5'ss of exon 3
GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttttttcgtagaggaaactctcacacctg---ttttggttttttaattgttaatttgtag-------------------------
||||||||||| ||||||||  |||||||||||||||| || ||||||||  | |||||||| ||||||||  | ||||||||  |||  | |   || ||  | || |  || || ||   ||| || |   |  |    | | | |    ||   |||| |  | ||     |  ||||  ||                         
GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCTATTAGAGATGTTCAGGAAGCTAGCGTCTATGAGGgtatcatttcattcctctcttttatgtttctttgacctttgttataattctac---attataaagtttggatttttagactattggcattagatttccagcttgattgaatcatgtaattgacag

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 5'ss of exon 3
GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttttttcgtagaggaaactctcacacctgttttggttttttaattgttaatttgtag
||||| || || ||||||||||| |||||||||||||| || || ||||| ||  | |||||||| ||||| ||||| |||||   || ||||  || | |  || |    |   |||  || || ||| | ||   |   |  | |  |  |  | |  |||| || |||| ||       
GACAAAGCTATTAAGAGGTTTCTGGTGAGGAACATTGTGGAGCAAGCTGCTGTTCGTGATGTGCAAGAAGCTTGTGTTTATGA---TAgtaattcttctttatcaatactttctatcttcttcttctttatggtgatgatgatccactgagtt--tgtatttttctacttgtgaag------

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv13s0067g02700.t01 (Vitis vinifera), 5'ss of exon 4
GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattt-tcttacattc---accttactctgttttttttttttcgtagaggaaactctcacacctgttttggttttttaattgttaatttgtag
|||||||| |||||||||||| | ||||||||||| || || || |||||||| || ||||| ||||| ||||| ||||||||  ||||| | | ||  ||||   |||   |  ||  ||||| |||||| | |  |   ||     || |  |    | | |                      
GACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACAgtaattacacttcctctttttttcggtaatttgttctgtgttttttatctgatttggggg---ctaattctctgtgtag----------------------

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|19269126|gb|BM885382.1|BM885382
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGNACTGGTGTT-CCTGT
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTG-TGTTTCCTGT
EST: gi|6070885|gb|AW100272.1|AW100272
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACCCCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGT
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGC-TTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGT
EST: gi|192326591|gb|FK018838.1|FK018838
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|298198055|gb|HO039594.1|HO039594
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|26058129|gb|CA801043.1|CA801043
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|9205491|gb|BE331715.1|BE331715
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|31465608|gb|CD407636.1|CD407636
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|10238902|gb|BE807798.1|BE807798
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|151411510|gb|EV281321.1|EV281321
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|298192759|gb|HO033193.1|HO033193
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGAAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|31466786|gb|CD408814.1|CD408814
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|298183541|gb|HO028754.1|HO028754
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|298182602|gb|HO031337.1|HO031337
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|298162975|gb|HO011708.1|HO011708
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGTAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|17023090|gb|BM094124.1|BM094124
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|192296480|gb|FG992316.1|FG992316
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|298197741|gb|HO045220.1|HO045220
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|4405733|gb|AI507882.1|AI507882
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|298163646|gb|HO012379.1|HO012379
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|31474104|gb|CD416132.1|CD416132
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|21601683|gb|BQ612014.1|BQ612014
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC                         AATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataa ... taatttgtagAATACACGCTTCCGAAACTATATGTGAAGATGCAGTACTGTGTTTCCTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAACgtaataataattttcttacattcaccttactctgttttttttttttcgtagaggaaactctcacacctgttttggttttttaattgttaatttgtag

- - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG