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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caactttcatatttatgtgctttatgggacaaataagttcttacaaagtagaagattctcataaaacatgattgtgaaatcattacctgtacttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACC

Basic information

species Zea mays
transcript GRMZM2G160458_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160458_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 4
---caactttcatatt-tatgtgctttatgggacaaataagttcttacaaagtagaagattctcataaaacatgattgtgaaatcattacctgtacttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACC
   |     | |  || ||  |||||  |     |   |||   ||   ||  | |     |  | ||||||| |      ||  ||||  ||  ||    ||||||||||||||||| |||||||| || || ||||| ||||| ||||||||||||||||||||||| || || |||| ||||||||||||| |||| || |
aatccgtgatgaagttatacatgcttcttttc-tagtaaagcagttgagaaacaaacttgccctaaaaaacataagaaactaactattatttgctctg---cagATATTTGCTACTCCAAAAGATCATCGAAAGGCAAAGCCTTTTCATGACCATGTGTTTGTCTTCTCTATCGTTGATGACCATGTTTGGTTTAGAAATTATC

upper sequence: GRMZM2G160458_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G15460.1 (Arabidopsis thaliana), 3'ss of exon 4
caactttcatatttatgtgctttatgggacaaataagttcttacaaagtagaagattctcataaaacatgattgtgaaatcattacctgtacttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACC
    | ||||  | |  |      || |    ||   ||  ||         || ||    || | | | |   |  ||   ||   | |     | ||||| ||||  | |||  | |  ||  | ||  | ||||||| |||||||||||||||||| ||||||||||| |||| |||| | ||||| || || ||||
---gtctcattctcacttttgaattgtggacgatccttttgtagtcgcggttagtttggtttatatcttcaacttttaagttttgtttttttgcttacagATTTTTGGAATTCCCGAGGGACATAGGAAGTCTAAACCTTACCATGACCATGTGTTTGTTTTCTCCATTGTTGATGACCATATATGGTTCCGTAATTACC
















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|71429209|gb|DR810259.1|DR810259
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTTCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|148946148|gb|EC891442.2|EC891442
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|148946147|gb|EC891441.2|EC891441
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAATTCAG                         ATATTTGTTACTCTTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|148996317|gb|EE035601.2|EE035601
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|149070865|gb|EE159274.2|EE159274
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|50323762|gb|CO518888.1|CO518888
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|110196089|gb|EC877986.1|EC877986
EST:     GGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGTTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: GGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|71429925|gb|DR810975.1|DR810975
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|71301915|gb|DR787034.1|DR787034
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|50326773|gb|CO521899.1|CO521899
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACC
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACC
EST: gi|78089924|gb|DV518298.1|DV518298
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACC
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACC
EST: gi|60347622|gb|DN214595.1|DN214595
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|71429926|gb|DR810976.1|DR810976
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|78089923|gb|DV518297.1|DV518297
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|211002651|gb|FL371731.1|FL371731
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|149070866|gb|EE159275.2|EE159275
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAGATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|32842309|gb|CD981990.1|CD981990
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTAGTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATG
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATG
EST: gi|50332851|gb|CO527977.1|CO527977
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|71426064|gb|DR807114.1|DR807114
EST:     ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: ATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
EST: gi|86469691|gb|DY236061.1|DY236061
EST:     TTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAG                         ATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT
genomic: TTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCAT

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), 48 (downstream exon)
Score: 240

TACCGGTAACCATCTGAAAGGGTCACGCCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

TACCGGTAACCATCTGAAAGGGTCACGCCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 136

TACCGGTAACCATCTGAAAGGGTCACGCCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 55

TACCGGTAACCATCTGAAAGGGTCACGCCCACTTCTTACATTTTCTACAAATTTTGATGAGCAACCTCATTGGAAGCTTGTGAAGGAAATGATAACTCAGgtatgtaact ... acttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtagaagattctcataaaacatgattgtgaaatcattacctgtacttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACC
                                              cttgtcc  CT-rich tract
               ataaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caactttcatatttatgtgctttatgggacaaataagttcttacaaagtagaagattctcataaaacatgattgtgaaatcattacctgtacttgtccagATATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACC

- - -ttcatat
- - - - - - - -tgtgctt
- - - - - - - - - - - - - ggacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatt