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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaatagtaaatatgggagtacgatctcattacttaaataaaatcttctacgtaatttggtttagtttatttagctttaatttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG

Basic information

species Glycine max
transcript GLYMA12G29800.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 12
gtaaatagtaaatatgggagtacgatctcattacttaaataaaatcttctacgtaatttggtttagtttatttagctttaatttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
                 |  | |        |||||   ||    ||| | |  |  |   ||   | | | | |||     ||   ||  | ||||||||| |||||||| ||||| |||||  ||||||| ||||||||||| ||||||||  ||||||||||||||||||||
-----------------gtatgcagcacacatacttgtctacgg-cttttgcccatatcatttccatctgtctggct---gattattttaatctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG

upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 12
gtaaatagtaaatatgggagtacgatctcattacttaaataaaatcttctacgtaatttggtttagtttatttagctttaatttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
            ||| ||  |||  | |   |  ||||||   | |  |   |||        |  |  || |       |  ||  || |   || ||||| || || ||||| ||||| ||  |||||||||| ||||||||||| |||||  |||| ||||| |||||||||
-----------gtataggt-taccttttggctg-ttaaatttcaccggcctggtagaacttcattatgaatatgctcaccaaatgctttgtgcatttcagCCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG

upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 12
----gtaaatagtaaatatgggagtacgatctcattacttaaataaaatcttctacgtaatttggtttagtttatttagctttaatttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG-------------------------
       |  |  |  |||  || ||| ||||  ||| | |  | |  ||  ||    |  |   |  |   || |    |||| | |  |||   || |  |||| || ||||| || ||||| ||  ||||| | ||||||||||||||||||| | ||||||| ||||||||||||                         
tagcagcatcaacagttatatgattaccatct--ttattaatgtgatttcgactttagagctatatgca--ctactctcttttactctctatttaattatatagCCGGCTCATGAGAAGATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAAGCAGTTCCTTCACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCAC

upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G801369_T03 (Zea mays), 3'ss of exon 12
gtaaatagtaaatatgggagtacgatctcattacttaaataaaatcttctacg--taatttggtttagtttatttag----ctttaatttgaa-ttcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
         |   |       |   || |  |  ||| ||   |||  | ||    | |   |||||  | ||  ||    || | || |||  || | ||   |||||||| ||||| |||||||| ||  |||| || || ||||||||||||||||| || ||||| ||||| ||||||
------gccatccacaacctgagcttccccctctttacatgctatccaccacaaccagtcatgttta-ctgatccaggattctcttatctgatcttatgttaaacagCCAGCCCATGAGAAAATTGGAGTGGTTGACTCCCAGTGGATTGTTCATCAAGTCATCCCTTCGCTTGGTAACCAG

upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 12
gtaaatagtaaatatgggagtacgatctcatt--acttaaataaaatcttctacgtaatttggtttagtttatttagctttaa---tttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG-------------------------
      |  |  |||  || ||| | || | |  |  |   |   |  || || |  || ||      | || | ||||   |   ||| | ||   || | ||||| || ||||| |||||||| ||  ||||| | ||||||||||||||||||  | ||||||| ||||| ||||||                         
----tcaacagttatatgattaccaacttaattaatgtgctttcgactttatatgctatatg-cacgatgtactgagctgggactcttttactttaattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCAC

upper sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 12
--------gtaaatagtaaatatgggagtacgatctcattacttaaataaaatcttctacgtaatttggtttagtttatttagctttaatttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
         || ||  |   | ||||   || | ||  |||     |    |||| ||   || ||    | |  | |  ||  | | | | ||  | || ||| ||||| |||||||| ||||| |||||  |||||||||| |||||| ||||| ||||| | ||||||||||||| ||| 
cagatattttatatttttcttttgggctaacaacctttttatcagca----atctactttctatttgacatcaactca--taattgttactgga--ttttctttacagCCTGCACATGAGAAAATCGGTGTGGTTGATTCACAGTGGATTATTCATAAAGTAGTACCTTCTCTTGGGAGCCAA

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|51343480|gb|CO984213.1|CO984213
EST:     ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAG                         CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
genomic: ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAGgtcagtaaat ... ttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
EST: gi|51338123|gb|CO981989.1|CO981989
EST:     ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAG                         CCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA
genomic: ATCTAGTGCATGGATGGGGATTGGACTTTGCTCTCAGAAGATGTGTAGAGgtcagtaaat ... ttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctacgtaatttggtttagtttatttagctttaatttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG
                              ctttaat  putative branch site (score: 4)
                                          ttcttttttgc  putative PPT
                tttagtttatttagct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatagtaaatatgggagtacgatctcattacttaaataaaatcttctacgtaatttggtttagtttatttagctttaatttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG

- - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaattc