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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagactcaataagataccattatctcctattgacttaggtaattcttatacttataattcttctacctttaattttattgaactgtttgttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC

Basic information

species Zea mays
transcript GRMZM2G006130_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 10
acagactcaataagataccat-tatctcctattgacttaggtaattcttatacttataattcttctacctttaattttattgaactgtttgt-tttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC
||  |  ||| || ||||||  |||||  |  | | ||  |  | | |  || |||| ||    | || |||  |||            ||| | ||||||||| |||||||||||||| |||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||| ||||  |||||| 
acctatccaagaaaataccaaatatcttttccttaattgag--actatggtagttatcataacaccacttttgttttgggaacgtctcctgtctctctacagGACGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCGACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAAT

upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 10
acagactcaataagataccat-tatctcctattgacttaggtaattcttatacttataattcttctacctttaattttattgaa-----ctgtttgttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC
       ||| || |||| |  |||||  | |||| ||    |  | |  ||||| |  |    | |  |||   |||    |       ||||   | ||||||||| |||||||||||||| |||||||||||||||| |||||||||||||||||| |||||||| ||||||||||||||||| ||||| ||||  |||||| 
----taccaagaaaatactaaatatcttttcttgaattga--agctatgttacttgtcgtaacaccagttttttgtttgggaacatctcttgttgtctctctacagGACGTATTGGACAGTCTAGAATTTGCAAGGGGGAATGCAGATTCAACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCCGAACCATTCCCTGTCAAAT
















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|18654845|gb|BM499650.1|BM499650
EST:     TAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     TAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|211150003|gb|FL374637.1|FL374637
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924051|gb|CF028863.1|CF028863
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924623|gb|CF029435.1|CF029435
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     TAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924613|gb|CF029425.1|CF029425
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|18661865|gb|BM501621.1|BM501621
EST:     TAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|211221447|gb|FL389601.1|FL389601
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGGAGTGCAGATTCAACATG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGG-AGTGCAGATTCAACATG
EST: gi|32923839|gb|CF028651.1|CF028651
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32929408|gb|CF034220.1|CF034220
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGCCAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|21331549|gb|BQ486930.1|BQ486930
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGTCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924017|gb|CF028829.1|CF028829
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32929966|gb|CF034778.1|CF034778
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924183|gb|CF028995.1|CF028995
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32928349|gb|CF033161.1|CF033161
EST:     TAAGCCACAATGATGAAGTCGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|18963147|gb|BM660266.1|BM660266
EST:     TAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|211079656|gb|FL402147.1|FL402147
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGNCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG

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: 29 (upstream exon), 49 (downstream exon)
Score: 143

GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 676

GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 480

GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 338

GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatacttataattcttctacctttaattttattgaactgtttgttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC
                      ctttaat  putative branch site (score: 338)
                                         tttgttttct  putative PPT
       ttataattcttctacc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagactcaataagataccattatctcctattgacttaggtaattcttatacttataattcttctacctttaattttattgaactgtttgttttctacagGATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaactg