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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaatcgtattctttttaattcacttctaggaaaaagaaactacgtaatctgcatgctataattagggccggatatcgagctagcttggctcgtt...

Basic information

species Zea mays
transcript GRMZM2G060999_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060999_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g32350.1 (Oryza sativa), 5'ss of exon 5
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtat------tcaaatcgtattctttttaattcacttctaggaaaaagaaactacgtaatctgcatgctataattagggccggatatc-gagctagcttggctcgtt
|||||||||||||||  |||||||| ||| | ||||| ||||||||| |||||||||||||||||||||| |||||||||||||| || ||||| |||||||||      | ||     ||  ||| |||||  | |     ||  |  |     |   ||  ||||||||  |||   |   || || |||||   | |       
GCCTTGTTGAATATGCCGAGGGAGACTGTGTCCGTATTCTTCCATGCAATCATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatggattaatctaaataatttataatttgcataagtaaatgaacagaactgcggtcaacatgctattgttacctctttatgtcagagctctatag-------

upper sequence: GRMZM2G060999_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G35490.1 (Glycine max), 5'ss of exon 5
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaatcgtattctttttaattcacttctaggaaa--aagaaactacgta---atctgcatgctata-attagggccggatatcgagctagcttggctcgtt
||||||| || ||||| || |||||  |  | ||  | || || || |||||||||||||||  |||||||||||| || ||| | ||||||||||||||||||     |  ||     ||   |   ||| | |  ||  |     |||   |   || |  ||   ||  |||      |  ||||||   |  | ||      
GCCTTGTGGAGTATGAGGATGGAGACAGCATGCGAGTTCTGCCTTGTCATCATGAATTTCATACAACATGTGTAGACAAGTGGCTGAAGGAGATTCACAGgtatgtgggt-atagggagttgggtgtccttttggataattatatggctaaaaacaaatttatataaaatttattgctatggtgtatcgattcatatcggg-----

upper sequence: GRMZM2G060999_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G17110.1 (Glycine max), 5'ss of exon 5
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaatcgtattctttttaattcacttctaggaaa--aagaaactacgtaatc-tgcatgctataattagggccggatatcgagctagcttggctcgtt-
||||||| || ||||| || |||||     | ||  |||| || ||||||||||||||||||  ||||||| |||| || ||| | ||||||||||||||||||   ||   ||    ||| | ||  ||||| |  ||  |  ||||| || | |  ||||  ||   | |      |  ||  |   || ||  ||   |  
GCCTTGTGGAGTATGAGGATGGAGACAACATGCGAGTACTACCGTGCCATCATGAATTTCATAGAACATGTATAGACAAGTGGCTGAAGGAGATTCACAGgtatgtgaaa-ataggaatttgagttttcttcttgttaactataaaacttcgaatttatgcaaactcccaatttactggtgtactg---tatctatgcatatct

upper sequence: GRMZM2G060999_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G35060.1 (Glycine max), 5'ss of exon 7
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaatcgtattctttttaattcacttctaggaaaaagaaactacgtaatctgcatgctataattagggccggatatcgagctagcttggctcgtt--
||||||| || ||||| || |||||  |  | ||  | || || || |||||||||||||||  |||||||||||| || ||| | ||||||||||||||||||     |        ||   | ||  ||     ||  | |        ||  |  |  |||||  ||        |   | | |   |    || |   
GCCTTGTGGAGTATGAGGATGGAGACAGCATGCGAGTTCTGCCTTGTCATCATGAATTTCATACAACATGTGTAGACAAGTGGCTGAAGGAGATTCACAGgtatgtgggtatagggagttgggagtccttttggataactatatggctaaaaacttcaaatctata--taaaatttactgctgtggtgtatcaattcatatc

upper sequence: GRMZM2G060999_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G08260.1 (Glycine max), 5'ss of exon 8
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtatt-caaatcgtattctttttaattcacttctaggaaaaagaaactacgtaatctgcatgctataattag--ggccggatatcgagctagcttggctcgtt
|||||||||| ||||| || |||||     | ||  |||| || ||||||||||||||||||  ||||||| |||| || ||| | ||||||||||||||||||  || |   ||  | ||| | ||  ||||| |  ||    |       | |     | ||||  ||    | | ||| |    | |   |    |    
GCCTTGTTGAGTATGAGGATGGAGACAACATGCGAGTACTACCGTGCCATCATGAATTTCATAGAACATGTATAGACAAGTGGCTGAAGGAGATTCACAGgtatgacacaaaataagcatttgagttttcttcttgttaactatattggtaaattaaaacttctatcgttccttgacgggacagaaggttttatgaaata---

upper sequence: GRMZM2G060999_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT5G45290.1 (Arabidopsis thaliana), 5'ss of exon 5
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaatcgtattctttttaattcacttctaggaaaaagaaactacgtaatctgcatgctata-attagggccggatatcgagctagcttggctcgtt
||||||| ||||||||||| | ||| | | |  | | |||||| || ||||||||||| ||   ||| ||||||||||||||| | ||||||||||||||||||  |  |  |||    | | |         |  |  ||    |  | |  |  |  ||   || ||||      ||| |     | ||   ||     
GCCTTGTGGAATATGAAGAAGCAGACTCTATAAGGACACTTCCTTGTCATCATGAATTCCACAAAACCTGTGTAGATAAATGGCTCAAGGAGATTCACAGgtatgaatgtgatatataatgtgaagtttggtgacaactaattttccgcctttttggtgtgtactagattatctgatgatgtttttatggcgaagcag---

upper sequence: GRMZM2G060999_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT5G45290.2 (Arabidopsis thaliana), 5'ss of exon 5
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaatcgtattctttttaattcacttctaggaaaaagaaactacgtaatctgcatgctata-attagggccggatatcgagctagcttggctcgtt
||||||| ||||||||||| | ||| | | |  | | |||||| || ||||||||||| ||   ||| ||||||||||||||| | ||||||||||||||||||  |  |  |||    | | |         |  |  ||    |  | |  |  |  ||   || ||||      ||| |     | ||   |      
GCCTTGTGGAATATGAAGAAGCAGACTCTATAAGGACACTTCCTTGTCATCATGAATTCCACAAAACCTGTGTAGATAAATGGCTCAAGGAGATTCACAGgtatgaatgtgatatataatgtgaagtttggtgacaactaattttccgcctttttggtgtgtactagattatctgatgatgtttttatggcgaag------

upper sequence: GRMZM2G060999_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0087g00420.t01 (Vitis vinifera), 5'ss of exon 5
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtat----tcaaatcgtattctttttaattcacttctaggaaaaagaaactacgtaatctgcatgctataattagggccggatatcgagcta--gcttggctcgtt
||||||| || ||||| || |||||     | ||  |  | || ||||||||||||||||||   ||||||||||| || ||| |||| ||||| |||||||||    |||| | |   |||  || | |  |||  | |        ||    |||| ||||   |||     ||   | |  |     ||  | ||  |||   
GCCTTGTGGAGTATGAGGAAGGAGACAACATGCGGGTGTTACCTTGCCATCATGAATTTCATAGGACATGTGTAGACAAGTGGCTAAAAGAGATACACAGgtatgtggtcaatttggcgtctccttgaat--ctttgatgtctcgtttacagtataatatgcaca-tatgcacgggcgtgtaagttctattatcgtttatctc---

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|4621582|gb|AI612415.1|AI612415
EST:     AACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: AACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|110195219|gb|EC877116.1|EC877116
EST:     CATGAATTTCATTTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|5871596|gb|AW018067.1|AW018067
EST:     ATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCCCTGATTGG
genomic: ATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|148999940|gb|EE037001.2|EE037001
EST:     CATGAATTTCATTTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATTTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|71299450|gb|DR785731.1|DR785731
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|101398514|gb|EB821130.1|EB821130
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|78544416|gb|DV621914.1|DV621914
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGCTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|78122498|gb|DV540882.1|DV540882
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|32932120|gb|CF036932.1|CF036932
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGCTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|71325678|gb|DR799524.1|DR799524
EST:     CATGAATTTCATTTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATTTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|78076337|gb|DV504771.1|DV504771
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|71771687|gb|DR969624.1|DR969624
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATTTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|5847602|gb|AW000681.1|AW000681
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|101398512|gb|EB821129.1|EB821129
EST:     CATGAATTTCATTTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|60400728|gb|DN233535.1|DN233535
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|5525666|gb|AI861559.1|AI861559
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
EST: gi|20315421|gb|BQ169270.1|BQ169270
EST:     CATGAATTTCATCTAACATGTGTAGATAAATGGCTAAAGGAGATTCACAG                         GGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG
genomic: CATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGG

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), 45 (downstream exon)
Score: 57

GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGGAAAGGTCAGCTGATTCTGTCTCTTGAGAATGCAGCTTCCTACAGAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 30

GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGGAAAGGTCAGCTGATTCTGTCTCTTGAGAATGCAGCTTCCTACAGAGAAA


Block sizes: 37 (upstream exon), 47 (downstream exon)
Score: 15

GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGGAAAGGTCAGCTGATTCTGTCTCTTGAGAATGCAGCTTCCTACAGAGAAA


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 31

GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaat ... tgttttctagGGTTTGTCCACTTTGTCGTGGCGATGTCTGCAGATCTGATGCACTGATTGGAAAGGTCAGCTGATTCTGTCTCTTGAGAATGCAGCTTCCTACAGAGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtattcaaatcgtattctttttaattcacttctaggaaaaagaaactacgtaatctgcatgctataattagggccggatatcgagctagcttggctcgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagaaa