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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtaccactactcctgcaccccccacttgcgcattcacgtatcactcgctcagatctcggagctcccgttccagatctcgccatccctccgccccg...

Basic information

species Zea mays
transcript GRMZM2G176612_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176612_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtaccactactcctgcac-cccccacttgcgcattcacgtatcactcgctcagatctcggagctc-ccgttccagatctcgccatccctccgccccg
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| ||||||||||||||||||||||  | | | ||  | ||| | |  ||| |    |||   | |   ||||  | || |   || |  | | || |  ||       || | ||||  |    
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacccccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt--

upper sequence: GRMZM2G176612_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtaccactactcctgcaccccccacttgcgcattcacgtatcactcgctcagatctcggagctc----ccgttccagatctcgccatccctccgccccg
| |||||||| |||||||| |||||||| || || |||||||||||| |||| ||||||||||  |||||||| ||||| || ||||||| |||||| ||| |   |    ||  |  ||        | | | | ||     | |   |   | |  |   | |  |     | |||    || |     |    | |   | 
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttgt----ttgaatggtgaatctgtttgttgattttttatgtgcggaaatttgtatcggtttgcaatatgattgtgtggctgattct

upper sequence: GRMZM2G176612_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
-----CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtaccactactcctgcaccccccacttgcgcattcacgtatcactcgctcagatctcggagctcccgttccagatctcgccatccctccgccccg-
     | |||||||| |||||||| |||||||| || || |||||||||||| |||| ||||||||||  |||||||| ||||| || ||||||| |||||| ||| |   |    ||  |  ||        | | | | ||     | |   |   | |  |   | |  |   ||  | | |  |   ||   |  |   |  
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtttttgctgattttgt----ttgaatggtgaatctgtttgttgattttttatgtgcggaaattt--gtatcggtttgcaatatgattgtgtggctg

upper sequence: GRMZM2G176612_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 5'ss of exon 2
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgt--accactactcctgcaccccccacttgcgcattcacgtatcactcgctcagatctcggagctcccgttccagatctcgccatccctccgccccg
| |||||||| || ||||| |||||||| || || |||||||||||| |||||||||||||||  ||  | || || ||||| ||||||| |||||||||||    |  |     | |  ||        |     |  ||   || |     | |||  |    ||  |    || |   |   |   |   |        
CGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaattttgagttttggtggtttgatccatgatttagggttttggcagttcaatttggtgatttgatatttcgactagggttttgatttaagat--

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|50325053|gb|CO520179.1|CO520179
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|50324070|gb|CO519196.1|CO519196
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|26456800|gb|CA828383.1|CA828383
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|26559842|gb|CA832077.1|CA832077
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|20506864|gb|BQ279378.1|BQ279378
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|91875558|gb|EB405515.1|EB405515
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|211533911|gb|FL193997.1|FL193997
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|71325907|gb|DR799636.1|DR799636
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|148971581|gb|EE022297.2|EE022297
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|93015029|gb|EB640549.1|EB640549
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|149103312|gb|EE288690.2|EE288690
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|148962572|gb|EE013450.2|EE013450
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|101384752|gb|EB814422.1|EB814422
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|22819543|gb|BU499633.1|BU499633
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|31355549|gb|CD439906.1|CD439906
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|148950095|gb|EC895631.2|EC895631
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|78119544|gb|DV537928.1|DV537928
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACT
EST: gi|87157844|gb|DY402633.1|DY402633
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|149074062|gb|EE162404.2|EE162404
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|60395607|gb|DN228477.1|DN228477
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
EST: gi|71317539|gb|DR795496.1|DR795496
EST:     GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAG                         GTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT
genomic: GACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATT

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: 48 (upstream exon), 49 (downstream exon)
Score: 183

CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATTCGGAGGCAACAACCGGGCACATGCTTTCTTCAAGCAGCATGGATGGACC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 169

CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATTCGGAGGCAACAACCGGGCACATGCTTTCTTCAAGCAGCATGGATGGACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATTCGGAGGCAACAACCGGGCACATGCTTTCTTCAAGCAGCATGGATGGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 156

CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtacc ... tctttcgcagGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATTCGGAGGCAACAACCGGGCACATGCTTTCTTCAAGCAGCATGGATGGACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtaccactactcctgcaccccccacttgcgcattcacgtatcactcgctcagatctcggagctcccgttccagatctcgccatccctccgccccg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgccatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcccc