Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtcgaagtaattaacttgtgctgccagatttatatttctcatatttaattcacatgtataatgatatatgatgttggatgaaaaaattataga...

Basic information

species Zea mays
transcript GRMZM2G083716_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 10
GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagt-tgtcgaagtaattaacttgtgct---gccagatttatatttctcatatttaattcacatgtataatgata-tatgatgttggatgaaaaaattataga-------------------------------------------
||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||| || ||||| ||| ||| |   ||| |   ||| | |      ||||| || |||    |  ||||   | |   || | | || | || || |   |||    ||   |                                             
GTGGGAGCACAAACAGAGACCGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCTACCAAGgttagtctgttgttataactgctttgagatagaaatagattaatgtttgc--ttcttaaggaagaaaaattaaggtagtttgttgctcactgagttgatatcaacgttcttctggctttggatctttaaaccgcttcctctttgtcag

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtcgaagtaattaacttgtgctgccagatttatatttctcatatttaattcacatgtataatgatatatgatgttggatgaaaaaattataga
|| ||||||||||| || || ||||| ||||||||||||||||||||||| ||||| || |||||||| ||||| | ||      ||| ||    || |     |||    | ||  |   ||  | |    |  |||||  |   | ||| ||   |    |         
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgatttt-----gtattt---ctgaggcttgagaagcgtgttatttgcat--actcgtgaactataactaatcaggattttaattcttcag--------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 9
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 9
GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgta--agttgtcgaagta-----attaactt-gtgctgc-cagatttatatttctcatatttaattcacatgtataatgatatatgatgttggatgaaaaaattataga-----------------
|| ||||||||||| ||||| ||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||||    ||    ||  |     || || || |   | | | | ||| |   | |  |   | | |  | | |    |   || | |  |  | || ||    |  | |                 
GTCGGAGCACAAACTGAAACAGAACTTAAAGAAAAGAAATTGAGAGTGGAGGATGCCCTTAATGCAACAAAGgtactgtttaattaaacatgaccatcaatttagaaatactctgctttctccatttgttgcctcactgccctttgctcttgcatttaagttaaggtgtaactggttcaaaattttcaatattgttag

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 9
lower sequence: EFJ32217 (Selaginella moellendorffii), 5'ss of exon 9
GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtcgaagtaattaacttgtgctgc--cagatttatatttctcatatttaattcacatgtataatgatatatgatgttggatgaaaaaattataga
|||||||| ||||| ||||| || || |||||||||||| | ||||| ||||| || ||||||||||| |||||||  |  ||   |  | | |   |  | |  ||  |      || ||  |                                                  
GTGGGAGCTCAAACGGAAACCGAGCTGAAAGAGAAGAAGCTTAGAGTGGAGGACGCTCTAAATGCAACAAAGgtaatataccggtcttgtcacccgttttttctgcaattcctcgcttttcgcag-------------------------------------------------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 9
lower sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 9
GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttg-tcgaagtaattaac-ttgtgctgccag-atttatatttctcatatttaattcacatgtataatgatatatgatgttggatgaaaaaattataga
|| || |||||||| || || ||||||||||| |||||||| ||||| || |||||  | |||||||| ||||||| | | ||| | |    ||  ||||| ||  ||  |||| ||| |                                                       
GTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAGgtaaatagatcggattctggaatattgtggtgtaagtgtttaaattgcag-----------------------------------------------------

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|78080917|gb|DV509329.1|DV509329
EST:     AATTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|148983128|gb|EE029059.2|EE029059
EST:     CCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: CCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|211283747|gb|FL354677.1|FL354677
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|149099157|gb|EE185182.2|EE185182
EST:     TGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: TGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|33094001|gb|CF053995.1|CF053995
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGGGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|22545503|gb|BU097862.1|BU097862
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|60342862|gb|DN209835.1|DN209835
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|211360073|gb|FL471663.1|FL471663
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGGGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|87156784|gb|DY401573.1|DY401573
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|24934364|gb|CA452582.1|CA452582
EST:     AACTAAAAGAGAAGAAGTTGAGAATTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|32837828|gb|CD977506.1|CD977506
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGGGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|211268071|gb|FL357474.1|FL357474
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGGGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|71764883|gb|DR962820.1|DR962820
EST:     GTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGCGG
genomic: GTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|26558604|gb|CA830839.1|CA830839
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|22545873|gb|BU098247.1|BU098247
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|148961769|gb|EE012546.2|EE012546
EST:     AATGCAACTAAG                         GCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTTTTTTGCGG
genomic: AATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGG
EST: gi|120480889|gb|EH211078.1|EH211078
EST:     AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG                         GCTGCCGTTGAGGAAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCG
genomic: AACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGG-AAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCG

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: 287

GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 668

GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 386

GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtc ... ctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtcgaagtaattaacttgtgctgccagatttatatttctcatatttaattcacatgtataatgatatatgatgttggatgaaaaaattataga

- - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaaaaa