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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgtgtcattatatttagacatagctttgtttaccattcatttacttttacttgttttgaaggaaaaacataccaagtattgtttccttgacttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATTCTGTGAATTCAATGGCAGATGTCCTCGAGTTGATGAAT

Basic information

species Glycine max
transcript GLYMA05G37800.1
intron # 15
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 13
acgtgtcattatatttagacatagctttgtttaccattcatttacttttacttgttttgaaggaaaaacataccaagtattgtttccttgacttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATTCTGTGAATTCAATGGCAGATGTCCTCGAGTTGATGAAT---------------------
                 || |||  |   | |   | | |   || ||||     |    | ||||   || ||   |||| |||| || |||||| |||||||||||||| |||| |   |||||| |||||| | ||||||||||||||||  |||||| |||| || ||||   |||||||  | ||  | ||||                       
-----------------gatatatgtccatcttgtaatgagacacctttaaac-ctccacaagaaagtgattcct--tatt-tttctttaacttgcgcacacttgggattttgaatgccagCCAACCCAATGGGCTTGCTGTTCCTGATGCAACAATGCATCCTGTCAACTCAAGTTCAGATGTTATTGAACTAATGAGAACAGGACTTGAGAACAGATCT

upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 15
-----------------------------------------------------------------acgtgtcattatatttagacatagctttgtttaccattcatttacttttacttgttttgaaggaaaaacataccaagtattgtttccttgacttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATTCTGTGAATTCAATGGCAGATGTCCTCGAGTTGATGAAT
                                                                 |  ||  |    |   ||| || | | || ||       |||   |||||||  | ||   |      | | | |   |   ||||||| ||||||| ||| | ||||||||||| || |||  |||||||||| | || || ||||||||||| ||||||| |||||  ||||  | |||||| || ||  ||||||||
atatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgctattaggttttactaatgttct-gtggttgcgttcaatacaaaatttccttaacttgcatacATTAGGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAAT

upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 13
--------acgtgtcattatatttagacatagctttgtttaccattcatttacttttact-tgttttgaaggaaaaacataccaagtattgtttccttgacttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATTCTGTGAATTCAATGGCAGATGTCCTCGAGTTGATGAAT-----------------------------------------
        | | |  ||  |  |   |  ||  |  || |   |    |||| |  ||   | ||||  | |  | | |||  ||      ||||||| ||||||| ||||||||||||||||||||| |   |||||||||  | || |||||||||||||| ||||||||||| |  ||||  | |||||| || ||  ||||||||                                         
gtcctaataagagatatccttctctaatctaattaagtatttgacatttttattgatatcattttttttatgttacaaatattaa-----atttccttaacttgcatacacttgggatttggaatacttctttaccaaatggcctcgcagTTCCTGATGCAAGCATGCATTCTGTAAGATCAACTGAAGATGTTCTTGAACTGATGAATATTGGGTTGATGAATAGAACTGTTGGCGCCACAACCCTTAA

upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G63640.2 (Arabidopsis thaliana), 3'ss of exon 15
---------------------------------------------------------------------------------acgtgtcattatatttagacatagctttgtttaccattcatttacttttacttgttttgaaggaaaaacataccaagtattgtttccttgacttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATTCTGTGAATTCAATGGCAGATGTCCTCGAGTTGATGAAT-----
                                                                                 |  ||  |    |   ||| || | | || ||       |||   |||||||  | ||   |      | | | |   |   ||||||| ||||||| ||| | ||||||||||| || |||  |||||||||| | || || ||||||||||| ||||||| |||||  ||||  | |||||| || ||  ||||||||     
gtggttccagtcgaagatatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgctattaggttttactaatgttct-gtggttgcgttcaatacaaaatttccttaacttgcatacattagGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAATATTGG

upper sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 16
acgtgtcattatatttagacatagctttgtttaccattcatttacttttacttgttttgaaggaaaaacataccaagtattgtttccttgacttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATTCTGTGAATTCAATGGCAGATGTCCTCGAGTTGATGAAT--------------------------------------
                               ||| | |  || ||||     |||  ||||         ||||           | || |||||||||||||||||||||||| |||  | ||||||||||| || ||||| ||||||||||| |||||  |||| || ||||  ||||| || || || || ||||||                                      
---------------------------aaactactactttttaacttgcttctgtcatgaaatttttttgtacc-----------ctttaacttgcacacacttgggatttggagtaccactcaaccaaatggtttagCTGTCCCTGATGCAAGCATGCACCCTGTTAAATCAACCGCAGACGTACTGGAATTAATGAATATTGGATTAATGAATAGGGCTGTAGGAGCCACTGCGCT

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|18690748|gb|BM519596.1|BM519596
EST:     TATAACGAACAAGTTCGTGATTTACTATCAAGCAACGGTCCTCAAAAGAG                         ACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGC
genomic: TATAACGAACAAGTTCGTGATTTACTATCAAGCAACGGTCCTCAAAAGAGatatcctttt ... acttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttacttgttttgaaggaaaaacataccaagtattgtttccttgacttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATTCTGTGAATTCAATGGCAGATGTCCTCGAGTTGATGAAT
                                      ttccttgac  putative branch site 
                  aaaaacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgtgtcattatatttagacatagctttgtttaccattcatttacttttacttgttttgaaggaaaaacataccaagtattgtttccttgacttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATTCTGTGAATTCAATGGCAGATGTCCTCGAGTTGATGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttcc