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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacttaattttgtgatgtagtaaaacaattcaactacatattgtaatatttttcatatgtctgtgtataatcaaactctttgatgccaatgtcatgcagATTGACGATGATGAAAAAATTACAGTGATTGACTTTCCGCAGATGGTGTCTGTTTCTCACCGTAATGCCCAAAT

Basic information

species Zea mays
transcript GRMZM2G038309_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038309_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g66520.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------gcacttaattttgtgatgtagtaaaacaatt----caactacatattgtaatatttttcata-tgtctgtgtataatcaaactctttgatgccaatgtcatgcagATTGACGATGATGAAAAAATTACAGTGATTGACTTTCCGCAGATGGTGTCTGTTTCTCACCGTAATGCCCAAAT
                                                            || | ||    |||     ||| ||||||      |  |   ||   |||  || |  ||| ||||    |||  |     | | || |    ||||  |||||||||| |||||||| ||| ||||| |||||||||| ||||||||||| ||||||   || || |||||||| ||
gtattgcttcttgtaccttttataagttcacatagaattcactctttggttgcctgcaaacagtcaaacaggtgtcaaggtagaacaatggttgtagttttctagattaaacttctgaataatgtcaccatattttttctttgtgtg-tattgatgttttgcagATTGATGATGATGAGAAAGTTACAATGATTGACTTCCCGCAGATGGTATCTGTTAAACATCGGAATGCCCAGAT

upper sequence: GRMZM2G038309_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G04910.1 (Glycine max), 3'ss of exon 7
-------gcacttaattttgtgatgtagtaaaacaattcaactacatatt--gtaatatttttcat-atgtctgtgtataatcaaact-----ctttgatgccaatgtcatgcagATTGACGATGATGAAAAAATTACAGTGATTGACTTTCCGCAGATGGTGTCTGTTTCTCACCGTAATGCCCAAAT-
         || |       | |   | ||||  ||||| | |   ||||   | | ||   | ||  |||  |  | |  |   | |     || |||   | ||    || ||||| | |||||||||||||||||| ||||||| ||||| || ||||| ||||| || ||||||||||| || || 
tatgctttaacatgccagcataaatgattaaaggaattctaatttttatttcatgaaatcagttattgtgttggcttttgcttctagtttacactctgaattctattcattgtagaTTAATGATGATGAAAAAATTACAATGATTGATTTTCCACAAATGGTATCTGTGTCACACCGTAATGCGCAGATG

upper sequence: GRMZM2G038309_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G33320.1 (Glycine max), 3'ss of exon 7
----------gcac-ttaattttgtgatgtagtaaaac---aattcaactacatattgtaa--tatttttcatatgtctgtgtataatcaaactctttgatgccaatgtcatgcagATTGACGATGATGAAAAAATTACAGTGATTGACTTTCCGCAGATGGTGTCTGTTTCTCACCGTAATGCCCAAAT
           ||    |   |  ||||  |   ||     |||| || | |||    | |  |||| |       | ||  | |  |  | | |  |||   | ||    || ||||||| |||||||||||||||||| ||||||| ||||| || ||||| ||||| || ||||||||||| || ||
gtatgctttaacatgccagcataatgattaaaggaattctaaatttaatttcatgaaatcagttattctgttggcttttgcttctggttca-cacactgaattccattcattgtagATTGATGATGATGAAAAAATTACAATGATTGATTTTCCACAAATGGTATCTGTGTCACACCGTAATGCGCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatttttcatatgtctgtgtataatcaaactctttgatgccaatgtcatgcagATTGACGATGATGAAAAAATTACAGTGATTGACTTTCCGCAGATGGTGTCTGTTTCTCACCGTAATGCCCAAAT
                                 ctttgat  putative branch site (score: 5)
                     tataatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacttaattttgtgatgtagtaaaacaattcaactacatattgtaatatttttcatatgtctgtgtataatcaaactctttgatgccaatgtcatgcagATTGACGATGATGAAAAAATTACAGTGATTGACTTTCCGCAGATGGTGTCTGTTTCTCACCGTAATGCCCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - -tgtgatg
- - - - - - - - - - - aaaacaa
- - - - - - - - - - - - - - - - aactaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgcc