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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTGTTTGTTGCACAATCTTACAGCAAGAACCTTGGTTTATATTCTGAAAGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattcttttttttactgattgctgcttatccagcccccctcgacccaatttaattcagtagttggaaatgcttaggcaagcagaataggcaacccgttt...

Basic information

species Zea mays
transcript GRMZM5G836910_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836910_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 5'ss of exon 9
AAGTGTTTGTTGCACAATCTTACAGCAAGAACCTTGGTTTATATTCTGAAAGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt--ttttactgattgc-tgcttatcca----gcccccctcgacccaatttaattcagtagttggaaatgcttaggcaagcagaataggcaacccgttt
||||||||||||| || ||||| ||||| ||||||||||||||| | |||||  |||| ||||||||||| || |||||| |||| ||||| ||| | ||||  |  |||  | | | ||||||| | | ||  ||    |  |   || | ||| || | | |||    ||  |||  |     |  | |  |||           
AAGTGTTTGTTGCGCAGTCTTATAGCAAAAACCTTGGTTTATATGCAGAAAGAATTGGAGCAATAAATGTTGTCTGCTCAACACCTGAAGTCGCAAACAGgtgatactttaatctgaatgattgccttcgtagtcaaattgttcgtttctatccagtt-attgcagcgaatgttaataatagattattctgtttagtgggt------

upper sequence: GRMZM5G836910_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ26197 (Selaginella moellendorffii), 5'ss of exon 7
AAGTGTTTGTTGCACAATCTTACAGCAAGAACCTTGGTTTATATTCTGAAAGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattcttttttttactgattgc--tgcttatccagcccccctcgacccaatttaattcagtagttggaaatgcttaggcaagcagaataggcaacccgttt
|  ||||||||||||| || |||||||||||||||||  | ||  | |||||  |||||||||| || ||| |     || |  | ||  | ||||  ||||||  |       | |   | |  || | |  ||  |   || | |    ||| || |||                                         
AGATGTTTGTTGCACAGTCCTACAGCAAGAACCTTGGCCTCTACGCCGAAAGAATTGGTGCAATCAACGTCATTCTTCCAACGGCCGACTTGGCAGCAAGgtatgataaaacaaaatatctacggtgttaaaacactcgtgcttg-cttgctttgat-cag-----------------------------------------
















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|18169477|gb|BM339317.1|BM339317
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|32845644|gb|CD985325.1|CD985325
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCA
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCA
EST: gi|26557436|gb|CA829671.1|CA829671
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCG
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCG
EST: gi|149000840|gb|EE038068.2|EE038068
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|32863795|gb|CF003477.1|CF003477
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|78104307|gb|DV522725.1|DV522725
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|5342983|gb|AI795288.1|AI795288
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGNAAAGAGCCAGCTGAAACGATTGGCACG
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACG
EST: gi|18162138|gb|BM331977.1|BM331977
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|78114228|gb|DV532617.1|DV532617
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|76289790|gb|DV029358.1|DV029358
EST:     CAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: CAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|32844188|gb|CD983869.1|CD983869
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
EST: gi|32921476|gb|CF026288.1|CF026288
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTA
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTA
EST: gi|32926958|gb|CF031770.1|CF031770
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
EST: gi|32920753|gb|CF025565.1|CF025565
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
EST: gi|60356876|gb|DN223849.1|DN223849
EST:     GTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: GTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|32843721|gb|CD983402.1|CD983402
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTAC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTAC
EST: gi|60349017|gb|DN215990.1|DN215990
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|32925729|gb|CF030541.1|CF030541
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTA
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTA
EST: gi|32921723|gb|CF026535.1|CF026535
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTA
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTA
EST: gi|60347013|gb|DN213986.1|DN213986
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|13150003|gb|BG320325.1|BG320325
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAATAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|211493773|gb|FL172989.1|FL172989
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|32843163|gb|CD982844.1|CD982844
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTAC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTAC
EST: gi|32921739|gb|CF026551.1|CF026551
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
EST: gi|32925063|gb|CF029875.1|CF029875
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAACCAGCTGAAACGATTGGCACGTCCCATGTA
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTA
EST: gi|6827402|gb|AW331045.1|AW331045
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|32925965|gb|CF030777.1|CF030777
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTAC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTAC
EST: gi|5770276|gb|AI973450.1|AI973450
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|32925664|gb|CF030476.1|CF030476
EST:     AGGGTTGGTGCGATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGT
EST: gi|91056033|gb|EB166451.1|EB166451
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACTCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|18167109|gb|BM336948.1|BM336948
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
EST: gi|26557367|gb|CA829602.1|CA829602
EST:     AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAG                         GGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC
genomic: AGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCC

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), 47 (downstream exon)
Score: 109

AAGTGTTTGTTGCACAATCTTACAGCAAGAACCTTGGTTTATATTCTGAAAGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCCTATTCACGGTGCCAAGATAGTTGCCAACGTTGTTGGTGATCCAACCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 710

AAGTGTTTGTTGCACAATCTTACAGCAAGAACCTTGGTTTATATTCTGAAAGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCCTATTCACGGTGCCAAGATAGTTGCCAACGTTGTTGGTGATCCAACCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

AAGTGTTTGTTGCACAATCTTACAGCAAGAACCTTGGTTTATATTCTGAAAGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCCTATTCACGGTGCCAAGATAGTTGCCAACGTTGTTGGTGATCCAACCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 493

AAGTGTTTGTTGCACAATCTTACAGCAAGAACCTTGGTTTATATTCTGAAAGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattctttt ... ttcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCCTATTCACGGTGCCAAGATAGTTGCCAACGTTGTTGGTGATCCAACCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTGTTTGTTGCACAATCTTACAGCAAGAACCTTGGTTTATATTCTGAAAGGGTTGGTGCAATAAATGTCGTGTGCTCAGCACCAGAAGTTGCAGATAGgtattcttttttttactgattgctgcttatccagcccccctcgacccaatttaattcagtagttggaaatgcttaggcaagcagaataggcaacccgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagcagaa