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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgccttctttcttttctaatgttgtcccttaaattcaaccatacttattaggcttaaatatgttttaggtccctaatataaaaaaattgttgcat...

Basic information

species Glycine max
transcript GLYMA12G37130.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G37130.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 5'ss of exon 3
CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgccttctt-------tcttttctaatgttgtcccttaaattcaaccatacttattaggcttaaata--tgttttaggtccctaatataaaaaaattgttgcat
|||   ||||  | |  | |||||  | || || || ||||| |||||||| |||||||||||||||||||| | |   || ||       |  || |||   | ||     | || |||| || || | | |  | || |   | |  | | |  | | | ||               
CTCGCAGGATACGATAATAAGTTGTCTTGGGCTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtgaatttttttttagtttgattcttgctagcatagtttgcaatatacaactattctcagttgaatgaactggttatacttgatggc-agtgtag--------------

upper sequence: GLYMA12G37130.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G087692_T02 (Zea mays), 5'ss of exon 3
CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcctt---ctttcttttctaatgttgtcccttaaattcaaccatacttattaggcttaaatatgttttaggtccctaatataaaaaaattgttgcat-----------------------
|||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||||   |  |||   ||        | || |||      ||  ||  | | | |  | ||   || | ||     |   |   | |||  | |  | |||   |                       
CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttcttaacctgaaccagtttatattgctatgcaaggtct-ctacaatggtcagttatatacataaagaataccttaactattgatagctggttaattattaccttttccttgcagtgtag

upper sequence: GLYMA12G37130.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G087692_T01 (Zea mays), 5'ss of exon 3
CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcctt---ctttcttttctaatgttgtcccttaaattcaaccatacttattaggcttaaatatgttttaggtccctaatataaaaaaattgttgcat------------------
       |||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||||   |  |||   ||        | || |||      ||  ||  | | | |  | ||   || | ||     |   |   | |||  | |  | |||   |                  
-------GATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttcttaacctgaaccagtttatattgctatgcaaggtct-ctacaatggtcagttatatacataaagaataccttaactattgatagctggttaattattaccttttccttgcag

upper sequence: GLYMA12G37130.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G087692_T03 (Zea mays), 5'ss of exon 3
CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcctt---ctttcttttctaatgttgtcccttaaattcaaccatacttattaggcttaaatatgttttaggtccctaatataaaaaaattgttgcat------------------
|||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||||   |  |||   ||        | || |||      ||  ||  | | | |  | ||   || | ||     |   |   | |||  | |  | |||   |                  
CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAGgtacatttcttaacctgaaccagtttatattgctatgcaaggtct-ctacaatggtcagttatatacataaagaataccttaactattgatagctggttaattattaccttttccttgcag

upper sequence: GLYMA12G37130.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv18s0001g06830.t01 (Vitis vinifera), 5'ss of exon 5
CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgccttctttcttttctaatgttgtcccttaaattcaaccatacttattaggcttaaatatgttttaggtccctaatataaaaaaattgttgcat----
 ||| | ||| ||||  | || ||||||||||| || ||||| |||||||| |||||||| ||||||||||| |  || |  ||    || | ||| | |    ||   | | | ||   |   |  || |||  || |   |     |  ||    |    |  || |     
TTCTCTAGATCTGGTAATCAGCTGCTTGGGACTCCATTGGACGAATGATCTTCCTGGAGCCATGATACAGgtaa--gcttctttagagttgttatggttttaagtattgttatcgatgtct-caaaactcaaaagtgatg-ggcctggtgctacgctatgtcttctgaagtgca

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|193409851|gb|FK372063.1|FK372063
EST:     GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG                         TCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
genomic: GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcct ... tgttttgcagTCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
EST: gi|6846254|gb|AW348544.1|AW348544
EST:     GTTGCTTGGGACTACACTGGACTAATGATCTGNCTGGAGCAATGATACAG                         TNNAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
genomic: GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcct ... tgttttgcagTCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
EST: gi|14012032|gb|BG726963.1|BG726963
EST:     GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG                         TCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
genomic: GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcct ... tgttttgcagTCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
EST: gi|192297062|gb|FG990333.1|FG990333
EST:     GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG                         ---A--TTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
genomic: GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcct ... tgttttgcagTCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
EST: gi|15200173|gb|BI424211.1|BI424211
EST:     GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG                         TCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
genomic: GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcct ... tgttttgcagTCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
EST: gi|6071750|gb|AW101137.1|AW101137
EST:     TCTGCCTGGAGCAATGATACAG                         TCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
genomic: TCTGCCTGGAGCAATGATACAGgttactgcct ... tgttttgcagTCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
EST: gi|51335049|gb|CO978915.1|CO978915
EST:     GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG                         TCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
genomic: GTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgcct ... tgttttgcagTCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
EST: gi|192299412|gb|FG992530.1|FG992530
EST:     CCTGGAGCAATGATACAG                         TCTAGATTGGCATTGAGGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT
genomic: CCTGGAGCAATGATACAGgttactgcct ... tgttttgcagTCTAGATTGGCATTGAAGCCTGATGGCTTATTTTTAGCAGCTATTCTTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAGgttactgccttctttcttttctaatgttgtcccttaaattcaaccatacttattaggcttaaatatgttttaggtccctaatataaaaaaattgttgcat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA