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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG

Basic information

species Zea mays
transcript GRMZM2G461569_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
lower sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 15
--tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatgg-attgtacctgtcaattttctcatcatgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG
  |  |||| |  |     |  | |   |||  ||    |||||  ||| |||  | ||||  ||  | |       | ||  | |||||| |||||  |||||||||| || ||||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||||||||||||||| || ||||||||||||| |
ttttgtgttatacagacccttctattgttat--attgtggatattcgtttatgatactgtaaatgggactgactaagttataat-ttactgccttgtaaacagTGAAGGAGCAGGTGGTGGTCATGCTCCAGACATTATCAAAGTATGTGGAGTGAAAAATGTGTTACCCTCTTCAACAAATCCAACTCGGCCATTTACTTTG

upper sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 13
tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG
|     ||    || |    |       || | || | |||| ||||    | |   |  || |   ||  | |  |   | |     | |  ||| ||||||||| |||||||| || ||||||||||| ||||| ||||| ||||| |  || |||||  | ||||| ||||||||||| || || || | |||    
ttcccctgaaagctctaccattctttctttgaactataatatctgttttccggtctaagttggcttattcttgactaaactttattattttcttgggcagTGAAGGAGCTGGTGGTGGCCATGCTCCAGATATCATAAAAGTATGTGGTGAGAAGAATGTCCTACCCTCATCAACAAATCCCACACGTCCTTATACACAT

upper sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G10850.1 (Glycine max), 3'ss of exon 14
-tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACT-TCG----
  ||            || |      |   |    | || | | || |  |   |||||| || |   ||  | ||  | |   || ||| |  | ||    | |||||| ||||| |||||||||||||| || |||||||| |||||  | ||||||||  ||||||| |||||||| || || || || |||||| ||     
ccatcacaaatagaaatggaaaacacaatgtggcttttgttttctggtc-taagttgtacttggctgattcttgat-gtttctatattgtttacttga----gcagGTGCAGGTGGTGGTCATGCTCCAGATATAATCAAAGTATGTGGTATGAAAAATGTCCTGCCCTCATCAACAAACCCAACGCGCCCTTTTACTGTCAATAC

upper sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA05G27840.1 (Glycine max), 3'ss of exon 12
-tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtct-tgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG
  ||            || |    ||  ||    || | || |       |   |||||  || |   ||  | ||  | |   || ||| |   ||  |||||||||||| ||||| |||||||||||||| ||||||||||| |||||  | || |||||  ||||||| |||||||| || || || || || ||    
caatcacaaatagaaatggaa-aacacaatgcgacttttattttctagtctaagttgtatttggctgattcttgat-gtttctatattgtttacttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTATGAAGAATGTTCTGCCCTCATCAACAAACCCAACACGCCCTTTAACACTC

upper sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G67550.1 (Arabidopsis thaliana), 3'ss of exon 12
--------tattgttgtctactt-tgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtc-ttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG
          || |   ||  |  || |      | ||   ||  | |    |  |  | ||    |  | |  |  | ||  |  ||||  |    || || |||||||||||||||||||||| || ||||| ||||| ||||| | ||||||||| || ||||||||  | || || ||||| || || || ||||||| |||    
gttcatcagcttctcacctcttcatgcacctctcagatgcttccttcactgcttatgtttgaagcaaaatattgaagtgctatttttgtttgttaaatcattctggacagTGAAGGTGCTGGTGGTGGACATGCACCAGATATCATTAGAGTTTGTGGAGTGAAAAATGTACTCCCGTCATCAACCAACCCAACACGGCCATATACGAAA

upper sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcat-catgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG
| || |  | | ||    |      | |||     |   | |   ||  ||| || |   |||||   || | || ||| |          || ||  |||||||||||||||||| |||||||||||||| ||||||||||| ||||| || ||||||||  | ||||| || ||||| || || ||||| || ||||| 
ttttctaattttctgaaaataagatagattctatagccttttacattt-tggtttctttttgtcacacttttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC

upper sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
lower sequence: EFJ29500 (Selaginella moellendorffii), 3'ss of exon 10
tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG
                                   |||  |  | |       ||  || |||   |||||  |   ||    |    || |      |||||||| ||||| ||||| ||||| || ||||| ||||||||||||||  |   ||| ||  | || || || || ||||| ||| |||| || ||   |
-----------------------------------gtggaacttttcttctcgtttcacttgt---ttttccaactctggaagtgtc-tcgttctactagTGAAGGCGCTGGAGGCGGCCATGCCCCCGACATTATCAAAGTTTGTGGCCTTCCAAACGTTCTACCATCGTCCACGAATCCGACCAGGCCTTTCACCAAG

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|78085739|gb|DV514132.1|DV514132
EST:     GAGCATACAATCGCAGCTTTTAAAGGTAGAGCCATATATACATATCACAG                         TGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGT
genomic: GAGCATACAATCGCAGCTTTTAAAGGTAGAGCCATACATACATATCACAGgtatgaaaca ... ttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGT




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 36

GTCAATATACACACAGATACCTTAAATGAATCAGGCTGCGTGGAGCATACAATCGCAGCTTTTAAAGGTAGAGCCATACATACATATCACAGgtatgaaaca ... ttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 59

GTCAATATACACACAGATACCTTAAATGAATCAGGCTGCGTGGAGCATACAATCGCAGCTTTTAAAGGTAGAGCCATACATACATATCACAGgtatgaaaca ... ttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 65

GTCAATATACACACAGATACCTTAAATGAATCAGGCTGCGTGGAGCATACAATCGCAGCTTTTAAAGGTAGAGCCATACATACATATCACAGgtatgaaaca ... ttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 35

GTCAATATACACACAGATACCTTAAATGAATCAGGCTGCGTGGAGCATACAATCGCAGCTTTTAAAGGTAGAGCCATACATACATATCACAGgtatgaaaca ... ttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatggattgtacctgtcaattttctcatcatgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG
                                  ttcttac  putative branch site (score: 35)
                                        ctgtctt  CT-rich tract
                 tcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG

- ttgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttactg