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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaattaaaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt...

Basic information

species Glycine max
transcript GLYMA10G42940.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 8
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaatt---aaaatctg-ccaacgtca--ctattacat-catcaattaactttgttatt---tgaatgcagggactaaaagtggtgaccaagaaaaggt----------------------------------------------------------------------
 ||||| ||||||||||| || ||||| || || || || ||||||||||| ||||| ||||| || ||||||||| | || || ||||| || ||| |||||    |   | | ||   ||  ||||    |   ||   | |||        || ||| | || || |   |   |||      |     |||| |   |   |   |                                                                      
GTTTGCTGCTATGGGAGTGAATATGGAAACAGCCCAATTCTTCAAACGTGATTTTGAAGAGAACGGGTCAATGGAGCGGGTCACCCTTTTTCTGAATCTGgtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggctactctgtttacag

upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 8
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaattaaaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaa--agtggtgaccaagaaaaggt--
 ||||| ||||||||||| |||||||| || || || || ||||||||||| ||||| |||||||| || |||||| | || || ||||| || ||| ||||| ||    |  | ||   |  |   |||  ||  |||   | |||| || | ||  || |  |   ||    |  ||    |   ||    | |        
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCATGGAGCGGGTCACCCTTTTTCTGAATCTGgta-cctacaaggacttgtgaatttgtaac--caacattcatttatcattttatttc-ttctaagggcgccataatcaattctgcaatgttttacatgcatctt

upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaatta-aaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtg-gtgaccaagaaaaggt---
 ||||| ||||||||||| |||||||| || || || || ||||||||||| ||||| ||||| || || |||||  | || || ||||| || ||| ||||| ||    |  | |||  ||| ||  | |  || |  |  | |||   |||  | |   |   || |||    |       ||  |        |    |   
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgta-cctacaaggacttatgaatttgtgatcaacattcatttaccatt--ttatttctcccaa--gagtgccataatcggttctgcattgttttagatgcatatt

upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaattaaaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt
 || ||||| ||||| || ||||||||||||||||| ||||| |||||||| || |||||||||||||| |||||||||||||||||||||||||| |||| ||  ||    |||| | |  || |  || ||    ||  | ||    |||  |    | |||   || |||      |    ||   |   | |    
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctc--gcaatcaca--ctacagacatc----ttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag---

upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 8
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaattaaaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt----------------------
 ||||||||||||||||| ||||||||||||||||||||||| |||||||| || ||||| |||||||||||||||||||||||||| ||||||||  |||||    | | | |||||| ||  |      | | ||||   |  |    ||| ||    |||| ||  ||||    | ||  | || |   ||| || |                      
TTTTGCAGCTATGGGAGTAAACATGGAGACTGCACAGTTTTTTAAACGTGATTTCGAGGAAAATGGATCAATGGAGAGAGTGACTCTATTCCTTAACCTGgtatttatatta-aattaatata-gtggtatttattattgt-ttgtggtgtaaattctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacag

upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccc---tttaacaattaaaatctgcc-aacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt
 ||||||||||||||||||||||||||||| ||    || ||||||||||| || ||||| || || || |||||||||||||| ||||| || ||||||||| | |   |||||   | |   ||||   |||    | |  | ||| |||       ||||  |   | | |||  ||||    |  |  |        |  
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacggcaaagatatcttca-ccgtggttgtgttcctagttcaga-actagctcttattccttttccctg--

upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 7
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaattaaaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcaggg---actaaaagtggtgaccaagaaaaggt
                 ||||||||||||| ||    || ||||||||||| || || || |||||||| |||||||||||||| ||||| || || ||||||    ||| |   |||| ||      |   | |||  ||| |||      || |  | |  |   | | ||    |||     |||  | |  | |  | |
-----------------TTAACATGGAGACAGCTACTTTCTTCAAACGTGATTTCGAAGAAAATGGATCTATGGAGAGAGTGACACTTTTTCTCAACTTGgta--tgtttcaatcttaatattcctgtatccctctaccacagcattggagtacatactcaacttcgtcctggttgtactctggatgg-aagcgtggagtgtt

upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 7
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgta-accctttaacaattaaaatctgccaacg-tcactattacatcatca-attaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt---------------------------------------------------------------------------------------------------
 || || ||||||||||| |||||||| |||||    || |||||||| || ||||| || |||||||| |||||||||||||| ||||| || |||||||||    | |   || ||    | |  |  || |    |  ||||  |   ||||  | ||  | || | | |||   ||    ||  ||   ||||   |                                                                                                     
TTTCGCCGCTATGGGAGTGAACATGGAAACTGCCACTTTCTTCAAACGCGATTTTGAAGAAAATGGATCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatgtacatcttcagttttcttttatcgtcgattttcaccacatttttggattatatatggaacttca-tccagtttcttttcgtaatgg--aagagtcgtctgttttgagacttcacaaagtcaattttcctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgtcttgggctttcag

upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 7
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaattaaaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt
 |||||||||||||| || ||||||||||||||||||||||||||| | || |||||||| |||||||| ||||| ||||| ||  | ||| | ||  |||||   | |||   ||| | |  |||||| | |  | |||| || || ||    |||  ||                                       
CTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGATGGAAAGAGTCACATTGTTCTTAAACCTGgta---cgttatggattgacaa-tgccaatg-cgtttttac-tcctccatcgtgtttcgtacag------------------------------------

upper sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 7
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaattaaaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt
 |||||||||||||| || ||||||||||||||||||||||||||| | || |||||||| |||||||| ||||| ||||| ||  | ||| | ||  |||||   | |||   ||| | |  |||||| | |  | ||||  |  ||     ||| ||                                         
CTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGATGGAAAGAGTCACATTGTTCTTAAACCTGgta---cgttatggattgacaa-tgccaatg-cgtttttactcctccatcgtgcttcgtacag-------------------------------------

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|19452473|gb|BM953883.1|BM953883
EST:     CAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: CAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|120533616|gb|EH261749.1|EH261749
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTTCTTAAATTG                         TCCAATGATCCTACAATTGAACGTATTATCATTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16278890|gb|BI943147.1|BI943147
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|193355970|gb|FK322627.1|FK322627
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16277797|gb|BI942567.1|BI942567
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTATAC
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCT-TAC
EST: gi|16283207|gb|BI945427.1|BI945427
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|193430619|gb|FK396393.1|FK396393
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16278507|gb|BI942940.1|BI942940
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaattaaaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA