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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag

Basic information

species Zea mays
transcript GRMZM2G034143_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta-tcaacttttgccatg---tgttagggtgagtcaaattactaagatctattttttttttgcag
||| || || ||||||||||| || || |||||||| ||||||||||| ||||||||||||||||||||  ||||||||||||||||  ||||||| || |||| || ||||||| |||    |||| | || ||||||||||||||| |||  |  ||  ||||||
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattatttgttggagttagtcaaattactaagctct--tgattccttgcag

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 5'ss of exon 12
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta-tcaacttttg--ccatgtgttagggt-gagtcaaattactaagatctattttttttttgcag
||| || || ||||||||||| || || |||||||||||||||||||| ||||||||||||||||||||  | ||||||||||||||  ||||||| || |||| || |||||||     | |||| | ||  ||||| |||||| || |||  |  ||  ||||||
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttgtattgtttgttggagttaagtcacattactgagctct--tgattccttgcag

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA02G47270.1 (Glycine max), 5'ss of exon 12
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgc---------catgtgttagggtgagtcaa--attactaagatctattttttttttgcag-------------------------------
||| || || ||||| |||||  ||||||||||||| |||||||| ||||||||||| |||||||||||| | ||||| |||||||| |||||||| ||   | |     | |||         | |||||  |  | | |  |  || ||||   ||| ||||||||| |                                  
TGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtcatctgtgtgtgtgcttgggtatacctgtgtcggattcatttcatgatcactagtgtct-tttttttttggtgattcactaacttgtcctttgattattgagcag

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA18G08180.1 (Glycine max), 5'ss of exon 12
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag-----------------
||| || || ||||||||||| ||  ||||||||||||||||||| ||||||||||| ||| | |||||  | ||||| |||||||| || ||||| |  || |||  | | |    | || ||            | | |  |   || |    | ||                     
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGGt-tagttcatctgcatctatggtttggtacaaatctctgtttcatttggtgatactgacatcttatgctttgattaatgatcagc

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA14G01480.1 (Glycine max), 5'ss of exon 9
------TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctg--atttatcaacttttgccatgtgttagggtgagtca------aattactaagatctatt-ttttttttgcag--------------------------------
      ||| || || ||||| ||||| |||||||||||||| |||||||| ||||||||||| |||||||||||| | ||||| |||||||| |||||||| ||  ||||        |||   | |  |    ||| |||       || |||||  | |  | |||||||||  |                                
TTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtcatttgcgtgtgcttgg-gtatactgttttgattcatttcatgatcactaacttgtcctgttttttttggtgattcactaacttgtcctttgattattgagcag

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA08G45270.1 (Glycine max), 5'ss of exon 12
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag----------------
||| || || ||||||||||| ||  ||||||||||||||||||||||||||||||| ||| | |||||  | ||||| |||||||| || ||||| |  || |||  | | |    | || ||            | |||  |   || |  | | ||                    
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGgt-tagttcatctgcatctatggtttggtacaaatctctgtttcacttggtgatactgatatcttatgctttgatcaatgatcag

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 5'ss of exon 12
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag
 || || || |||||||| ||  |  |||||||||| ||||| || || |||||||||||||| |||||| | ||||| |||||||| |||||||| ||  || |   || |   |||   ||    | | |  | ||||||| | | | |     |   |||
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttcttt-ctctgctcatcacttctcctaact--atttactaacaacaaatggcactcaccag

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag---------------
 || || || |||||||| ||  |  |||||||||| ||||| || || |||||||||||||| |||||| | ||||| |||||||| |||||||| ||  || |   || |   |||   ||    | | |  | ||||||| | | | |     |   |||               
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttcttt-ctctgctcatcacttctcctaact--atttactaacaacaaatggcactcaccagcttatctacgagaag

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtc--tgatttatc---aacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag
||| || |||||||||||||||||||||||||| || |||||||| ||||| |||||||| || |||||  | ||||| |||||||| ||||||||    || | |     |  |  | ||| |||||  | |   |||   |  | |  ||| | |   | | ||||
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtcactcctatttcattccaggtgttctgtttcatca--ctgttgatgtctgtatcactgt-gcag

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag-----------------------------------------------------------
||| || || ||||||||||| || |||||||| || |||||||| || ||||||||||||||||| ||| ||||||| || || || || |||||  ||   |||  || |  |  ||| |    ||    ||   | |  |||   | |       ||||                                                            
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatct-ctctctctctgtatccttgtctccca---tgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag

upper sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
lower sequence: PP1S83_234V6.1 (Physcomitrella patens), 5'ss of exon 12
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta--tcaacttt------tgccatgtgttagggtgagtcaaat-tactaagatctattttttttttg---cag-----------------------------------------------------------------------------------
 || || ||||||||||||||  | || || ||||| ||||| || |||||||| |||||| | || ||||| |||||||| ||||| |||||||| | | | |  | ||   |      ||   |    ||   |      | | ||| || ||  | | ||  ||||   |||                                                                                   
CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAGgtatcagtcaatttaatcgtgttggatggtgttcactatttttccctgattgtacgaatattcactcttcatttggttcagtaatgatcagtcttagacttccagcgaggtcaacaatgcaactcatcctttgtttaggctgacttaatttttgcactttgcag

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|14311434|gb|BG901189.1|BG901189
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGCCAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|148943393|gb|EC888452.2|EC888452
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|32826219|gb|CD965897.1|CD965897
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|211032143|gb|FL160204.1|FL160204
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|37385350|gb|CF629812.1|CF629812
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|60340284|gb|DN207257.1|DN207257
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|110957674|gb|EE177726.1|EE177726
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|24766852|gb|CA401999.1|CA401999
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|67012645|gb|CO441394.1|CO441394
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|78113248|gb|DV531642.1|DV531642
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
EST: gi|211032142|gb|FL160203.1|FL160203
EST:     TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG                         CTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG
genomic: TAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTG

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: 49 (upstream exon), 48 (downstream exon)
Score: 50

TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTGTTGGACCCCATATTGGGAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 35

TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTGTTGGACCCCATATTGGGAACAG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 22

TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTGTTGGACCCCATATTGGGAACAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 66

TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgattta ... ttttttgcagCTCATCTATCAAAATTTACCAAAAGATATTGCAAATAGGCATGTTCTTCTGTTGGACCCCATATTGGGAACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA