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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACAGCACATCGCTCTCTCGATCTCAGCCATGGCGGAGGTGGAGCAGCCCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaatggctcttcacatctccacttcgatcgattctttagccatgctactgtgagcagtggattaaactccaatggaaaaaatctacag

Basic information

species Zea mays
transcript GRMZM2G078985_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078985_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 1
-GAAACAGCACATCGCTCTCTCGATCTCAGCCATGGCGGAGGTGGAGCAGCCCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaatggctcttcacatctccacttcgatcgattctttagccatgctactgtgagcagtggattaaactccaatggaaaaaatc-tacag
 |   | || |  |||   | |    ||||||||||| || |||||||  || ||| | | ||| |||||||||| ||||||| ||||||| || |||||||| ||    |  | | || | ||    || |   |   ||||  |||  |   ||    ||  |        ||||   ||         | |||
CGCCGCCGC-CGCCGCCACCGCAGCATCAGCCATGGCCGAAGTGGAGCTCCCGCAGCAGGAGGTCAAGCTCTTCAGCCGCTGGTCCTTCGAGGACGTCCAGgtgcgttggtt-cccctctcctccgtgctcctccctcctcttgggcccggtcgctaaccgcgtt--------ctccggcggcggcggcggtgcag

upper sequence: GRMZM2G078985_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv04s0043g00440.t01 (Vitis vinifera), 5'ss of exon 2
GAAACAGCACATCGCTCTCTCGATCTCAGCCATGGCGGAGGTGGAGCAGCCCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgt---acgcgaatggctcttcacatctccacttcgatcgattctttagccatgctactgtgag---cagtggattaaactccaatggaaaaaatctacag-
  |||||   |      |  |   |   ||| ||   || |  ||| ||   |    ||  |||||||||||||||||||||| ||||||||| ||||||||   |  ||      | |||  |  |   |   |      |  | | | | | |  ||   |   || | | ||| | ||   |||||    |       
CTAACAGAGGAGGAGAATGGCAGCCATTGCCGTGATTGACGATGAGAAGAAGCCCACCGAAGTGAAGCTCTTCAACCGCTGGAGCTTCGACGAAGTCCAGgttgaaatcgtgatatttttcttagtttttcaatggaaatctagtgaacaaagttgttgcatgtgccatttggttaga-tctgttggaagctttgagtttc
















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|211248101|gb|FL202300.1|FL202300
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAANCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|211241406|gb|FL202265.1|FL202265
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGC
EST: gi|211103280|gb|FL202207.1|FL202207
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|32912863|gb|CF017675.1|CF017675
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|91048196|gb|EB158614.1|EB158614
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|32914520|gb|CF019332.1|CF019332
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|32910202|gb|CF015014.1|CF015014
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGAC
EST: gi|211102230|gb|FL268198.1|FL268198
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|211241408|gb|FL202267.1|FL202267
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         -TGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAS-AC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|37424916|gb|CF650192.1|CF650192
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|211105749|gb|FL202215.1|FL202215
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|211103272|gb|FL202199.1|FL202199
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|14529575|gb|BI096708.1|BI096708
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|211105746|gb|FL202212.1|FL202212
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAA-CGA
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGC-A
EST: gi|211248104|gb|FL202303.1|FL202303
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGA
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGA
EST: gi|211243639|gb|FL202280.1|FL202280
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|211243630|gb|FL202271.1|FL202271
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|32908846|gb|CF013659.1|CF013659
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|149050421|gb|EE155667.2|EE155667
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|211243638|gb|FL202279.1|FL202279
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|211236925|gb|FL202231.1|FL202231
EST:     CCCAKGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGA
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGA
EST: gi|193503170|gb|AM937582.1|AM937582
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|32914057|gb|CF018869.1|CF018869
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGATCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGATCGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|32913186|gb|CF017998.1|CF017998
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|32944026|gb|CF048845.1|CF048845
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|32910541|gb|CF015353.1|CF015353
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|211239156|gb|FL202242.1|FL202242
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAMS-AC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|148932144|gb|EC875571.2|EC875571
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|32916229|gb|CF021041.1|CF021041
EST:     CCCGGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACCACCTGGCTGTGAGTGGGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
EST: gi|116826144|gb|EC869901.1|EC869901
EST:     CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAG                         GTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC
genomic: CCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCAC

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), 49 (downstream exon)
Score: 768

GAAACAGCACATCGCTCTCTCGATCTCAGCCATGGCGGAGGTGGAGCAGCCCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCACGCGACATTCCTGCCGCACTCCGCGGGGCGCTACTCCAAGAAGCGGTTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 244

GAAACAGCACATCGCTCTCTCGATCTCAGCCATGGCGGAGGTGGAGCAGCCCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCACGCGACATTCCTGCCGCACTCCGCGGGGCGCTACTCCAAGAAGCGGTTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

GAAACAGCACATCGCTCTCTCGATCTCAGCCATGGCGGAGGTGGAGCAGCCCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCACGCGACATTCCTGCCGCACTCCGCGGGGCGCTACTCCAAGAAGCGGTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 305

GAAACAGCACATCGCTCTCTCGATCTCAGCCATGGCGGAGGTGGAGCAGCCCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaat ... aaatctacagGTGAACGATATCTCGCTGAACGACTACCTGGCTGTGACTGCGGCGAAGCACGCGACATTCCTGCCGCACTCCGCGGGGCGCTACTCCAAGAAGCGGTTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACAGCACATCGCTCTCTCGATCTCAGCCATGGCGGAGGTGGAGCAGCCCCAGGACGCGGTGAAGCTCTTCAACCGCTGGACCTTCGACGATGTCCAGgtacgcgaatggctcttcacatctccacttcgatcgattctttagccatgctactgtgagcagtggattaaactccaatggaaaaaatctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA