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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

atatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgctattaggttttactaatgttctgtggttgcgttcaatacaaaatttccttaacttgcatacATTAGGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAAT

Basic information

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

upper sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 16
atatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgct-attaggttttactaatgttct-gtggttgcgttcaatacaaaatttccttaacttgcatacATTAGGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAAT
                   ||        |    | ||||| |  | |||     ||||||        |  |    |   ||  ||  |  | |||||    | |||   |||||||  | ||   |      | | | |   |   ||||||| ||||||| ||| | ||||||||||| || |||  |||||||||| | || || ||||||||||| |||||||                                      
-------------------tacttcatgcatctttattttgtatcatgtatgacagtgcat--------gtcattatatttaggcat-agcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACTTGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT--------------------------------------

upper sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 16
atatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgctattaggttttactaatgttctgtggttgcgttcaatacaaaatttccttaacttgcatacATTAGGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAAT--------------------------------------
                                                                                                      ||| ||  |||||      ||||||  |    ||   |   |     | |||||||||| ||| | ||||||||||  ||| |   |||||||||  |||| ||||||||||||||||||||   ||| | |||||| | ||| || || ||| | ||||||                                      
---------------------------------------------------------------------------------------------------aaactactactttttaacttgcttctgtcatgaaatttttttgta---ccctttaacttgcacacacttgggatttggagtaccactcaaccaaatggtttagCTGTCCCTGATGCAAGCATGCACCCTGTTAAATCAACCGCAGACGTACTGGAATTAATGAATATTGGATTAATGAATAGGGCTGTAGGAGCCACTGCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttactaatgttctgtggttgcgttcaatacaaaatttccttaacttgcatacATTAGGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAAT
 ttccttaac  putative branch site 
                         ttcaatacaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgctattaggttttactaatgttctgtggttgcgttcaatacaaaatttccttaacttgcatacATTAGGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG