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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaaatgcaattacttttctgggcagtaaaagtttattattctcttcccttggtttggtataaagtttacttctacttttttggagcagagcca...

Basic information

species Glycine max
transcript GLYMA12G29120.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaat--taaaatgcaattacttttctgggcagtaaaagtttattattctcttcccttggtttggtataaagtttacttctacttttttggagcagagcca
||| ||||| |||||  | ||  ||||||| || ||||||||||||||||| || ||||| |||||||| ||||| ||||| || |||||||| |||||||| ||   |  ||   || ||      |  |   |  ||    |       | |    ||   |||| |  |   | ||| ||    |       | |    
CCTTACACCTTCTGTTATCTCATTGATGGGTGGGCTGCTTCCCTTTGGCAGTATCTTCATTGAGATGTACTTTGTGTTCACGTCATTCTGGAACTACAAGgtaaacagtttaacttaagtatccaagtttgttttggaaacagaagtagtgcctatggtgtactggtgttcaacct-cttatatggctgcttcataaatta-

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa-atgcaatt--acttttctgggcagtaaaagtttattattctcttccc-ttggtttggtataa-agtttacttctacttt---tttggagcagagcca-------------------------------------------------------
 || ||||| |||||  | ||  ||||||| ||||| || ||||| |||||||| |||||||||||||| ||||| || ||||| |||||||| |||||||| ||  ||| ||   | |  ||  |  || ||  |   ||||     |||||  |   ||  |||| || || || |  | | |||  |   | || | ||     |                                                       
TCTTACACCCTCTGTTATCTCATTGATGGGTGGACTACTCCCCTTCGGCAGCATCTTCATCGAGATGTACTTTGTGTTTACTTCATTCTGGAACTACAAGgtaaagaaaacatatcagtgaacactaatgtgct-tctcagttctcacttctcaacaaattattttgctagaacagatggcatttacagtagatgtgtaccaacctaaaactctttttaatttgatggatagatagtaaccctatttctttggtatttggcag

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaaatgcaattacttttctgggcagtaaaagtttattattctcttcccttg---gtttggtataaagtttacttctacttttttggagcagagcca
|||||| || |||||  || | || ||||||||||||||||| ||||| ||||| ||||| |||||||| ||||| ||||| || || ||||| |||||||| ||  |     || | | ||| |    |||      || |||| |      || ||   |||  |  | | |  | ||||    |  |      | ||   
CCTCACGCCTTCTGTCATTGCCCTCATGGGAGGACTGCTTCCTTTTGGTAGCATCTTCATTGAGATGTACTTTGTCTTCACATCATTTTGGAACTACAAGgtaaaacaggcaacactaattttcccatacag----gcttcattactaaggagccctgagagttgagacttatgcatccttcctgatcatctattgacag---

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaaatgcaattacttttctgggcagtaaaagttta---------------------ttattctcttcccttggtt-tggta-taaagtttacttctacttttttggagcagagcca----------------------
||| ||||| |||||  |||| |||||||| ||||| || ||||| |||||||| ||||| |||||||| || |||||||||||||||||||| |||||||| ||  ||||    | |  |  |    | | ||||  |  |                      |   ||  |  ||||||    |||  |||||||  ||||  |  |||  || |                            
CCTTACACCTTCTGTTATTTCACTGATGGGTGGACTTCTCCCCTTCGGCAGCATCTTCATTGAGATGTACTTCGTATTCACTTCCTTCTGGAACTACAAGgtaaaaaaaaaacatagtggtgattgaagtactaaagatccaatcaccagcatatagaatgatctgcactactttcttggtcacagtagcaaagtttctttcttttagtttcaaggaatattgactccacttggtgccttggcag

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G026231_T01 (Zea mays), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaatta--aaatgcaatt----acttttctgggcagtaaaa--gtttattattctcttcccttggtttggtataaagtttactt--ctacttttttggagcagagcca
||| ||||| |||||  | ||  ||||||| || ||||||||||||||||| || ||||| |||||||| || || ||||| || |||||||| || ||||| ||  |  ||||||  ||    | |||| |   | || | |  | || |  | |   |  | |  | |  | ||| || | | |   |  ||  ||            
CCTTACACCTTCTGTCATCTCATTGATGGGTGGCCTGCTTCCCTTTGGCAGTATCTTCATTGAGATGTACTTCGTGTTCACATCATTCTGGAACTATAAGgtaaacgagcaaatgctttttaacatttttgtaccccgtgacatcgcttctcttaccactgtcatcttgtactgtaaggtgtgcatggttggttactttt----------

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaatta--aaatgcaat--tacttttctgggca--gtaaaagttt---attattctct-tcccttggtttggtataaagtttacttctacttttttggagcagagcca
||| ||||| |||||  | ||  ||||||| || ||||||||||| || ||||| ||||| |||||||| ||||| ||||| || |||||||| || ||||| ||  |  ||||||  |  |||  || ||  |    | | |  ||   |||  || || | |    ||   |||    ||  |  | |  ||||||            
CCTTACACCTTCTGTCATCTCATTGATGGGTGGCCTGCTTCCCTTCGGTAGCATCTTCATTGAGATGTACTTTGTGTTCACATCATTCTGGAACTATAAGgtaaacaagcaaatgcttttttacagttttgacctccttgagaccttgacattgctcactgtgctcctgtactgtacgttgtgcatgtttggtttttttt----------

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaaatgcaattacttttctgggcagtaaaagtttattattctcttcccttggtttggtataaagtttacttctacttttttggagcagagcca-
| | || ||||| || || || |||||||| ||  |||| |||||||| ||||| ||||| |||||||| ||||| ||||| |||||||||||||||||||| |||  |  | |  ||| |           ||     ||   | | ||||       || |  | |  |   |  | |  ||  |  |||     | | 
CTTGACTCCATCAGTCGTCTCCCTGATGGGGGGTTTGCTACCCTTTGGAAGCATCTTCATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAGgtaaatatagtttctcttaataagaacaaagttatggaattgcaaat-tcttattccaattggccaaaccggagagatttgattagtgagagactctcaac

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa--atgcaattacttttctgggcagtaaaagtttattattctcttcccttggtttggtataaagtttacttctacttttttggagcagagcca
 ||||||||||||||||| ||||| ||||||||||||||||| ||||| || || ||||| |||||||||||||| ||||| |||||||||||||| ||||| |||   |  ||    | | |  | |     | ||  | | |  ||| | |||| |  || | ||  ||  ||| |  |     |  || | |       
TCTCACACCATCTGTAGTCTCTCTCATGGGAGGACTGCTTCCTTTTGGGAGTATTTTCATTGAGATGTATTTTGTCTTCACATCCTTCTGGAATTATAAGgtaaatatgaccatttcttcaataatttaaat-gcaagtgatgagaattgttttccttgagtattgt-caagattttccccagtgctgctgcacctttattt

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 10
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaaatgcaattacttttctgggcagtaaaagtttattattctcttcccttggtttggtataaagtttacttctacttttttggagcagagcca------------
 |||||||||||||| || ||  |||||||||| ||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||||||||||||||||||      ||||  ||| ||| ||   ||    |   | ||  ||      | |  |||| ||  |  |||   | || |   ||| |  |  | | |              
TCTCACACCATCTGTTGTCTCAATGATGGGAGGTCTGCTACCCTTTGGCAGCATATTTATTGAGATGTACTTTGTCTTCACATCCTTCTGGAATTACAAGgt------aaatataatgactcttt--ggtttgagtggcttgctaaaaagatac--tggtgtg--agcaaggccatttttttatttgtaaatgaaaacattgcagtgtcttg

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 3
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaaat----gcaattacttttctgggcagtaaaagtttattattctcttcccttg-gtttggtataaagtttacttctacttttttg-gagcagagcca
| | |  || || || ||  | ||| |||||||  || | || || || ||||| |||||||||||||| ||||| ||||| || |||||| | |||||||||  |  |  |    |  |     |  | |||  | ||  || | ||  |         ||  |  ||  |   ||| |     || | |||| | |||      
CTTGAAGCCTTCGGTGGTGGCACTGCTGGGAGGGTTGTTGCCGTTCGGGAGCATCTTCATCGAGATGTACTTTGTGTTCACGTCGTTCTGGCAGTACAAGgtgggtggaggttggagggagcgggtggcagggtcggaagtgtgtgttggttgagcagagtgcatggggctttgggttgatggagacgtgtttgagggca------

upper sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 11
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaaatgcaattacttttctgggcagtaaaagtttattattctcttcccttggtttggtataaagtttacttctacttttttggagcagagcca
 ||||  |||||  | ||  | || ||||||||  | || || || || ||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||       |     | |||| |          ||| |  |  |||    || ||||       |                                
TCTCAAGCCATCCATCGTGGCGCTTATGGGAGGCTTACTCCCATTCGGGAGCATCTTCATAGAGATGTATTTCGTGTTCACGTCCTTTTGGAACTACAAGgt-aacccggtcgagcccagttttttc---------agtctgctgatctgagtccgtggtgcatggcag-------------------------------

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|193493779|gb|FK461425.1|FK461425
EST:     ATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: ATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
EST: gi|37995726|gb|CF807315.1|CF807315
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
EST: gi|16347100|gb|BI972695.1|BI972695
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGCTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
EST: gi|6341551|gb|AW164375.1|AW164375
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
EST: gi|26268557|gb|CA819620.1|CA819620
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCACACCATCTGTAGTTTCTCTGATGGGAGGACTGCTTCCCTTTGGCAGCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaaatgcaattacttttctgggcagtaaaagtttattattctcttcccttggtttggtataaagtttacttctacttttttggagcagagcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc