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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggctttcagtctttctgctccttttgccagttatagcagttctgacaaataagatgcaagttcatgtttcacaaactgctatatgtacaattt...

Basic information

species Zea mays
transcript GRMZM2G174730_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 3
GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggctttcagtctttctgctccttttgccagttatagcagttc-tgacaaataagatgcaagttcatgtttcacaaa-ctgctatatgtacaattt-
||| |||||||||||||||||||||||||||| ||||| ||||| ||||||||||||||| |||||||| | ||| || |   |    |  |||  || ||  |    | |  | ||||||    | | | || |||    | ||  || |  |    | ||||| 
GATTTGAAGAAAAAGGAGAAAGAACTCCAGGCAATGGAAGCTGAACTAAACAAAAGAGAAAGGgtgtgt-gccttacaattcctgatttaatttctcctgtgctctttgctggttacaaatcc--ttctattttatgaacaagaactctacagtcctgataatttc
















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|149076952|gb|EE165608.2|EE165608
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211455821|gb|FL370764.1|FL370764
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|32828156|gb|CD967834.1|CD967834
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211251918|gb|FL397021.1|FL397021
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAWGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|32825089|gb|CD964811.1|CD964811
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAGCGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|31353834|gb|CD438191.1|CD438191
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211137749|gb|FL292364.1|FL292364
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211138691|gb|FL292374.1|FL292374
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211198979|gb|FL379473.1|FL379473
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211039428|gb|FL384648.1|FL384648
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACCG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211501973|gb|FL392126.1|FL392126
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|149069546|gb|EE157919.2|EE157919
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|76927277|gb|DV171213.1|DV171213
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211138685|gb|FL292368.1|FL292368
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211138688|gb|FL292371.1|FL292371
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|4152018|gb|AI372152.1|AI372152
EST:     GAAAGATCTCCAGGCTATGGATGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGATGCGGCATCCCGAG
genomic: GAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211122269|gb|FL373644.1|FL373644
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|32825405|gb|CD965127.1|CD965127
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211138687|gb|FL292370.1|FL292370
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|76289053|gb|DV028621.1|DV028621
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|91872788|gb|EB402745.1|EB402745
EST:     AGGAGAAAGAACTCCAGGCTTTGGAGGCTGAGCTAAACAAAAGAGAAGGG                         GAATTGAAAAGGAAGGAAGAGGGGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|71322127|gb|DR797759.1|DR797759
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211228158|gb|FL414420.1|FL414420
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|32808007|gb|CD960241.1|CD960241
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|149079646|gb|EE168643.2|EE168643
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|78081465|gb|DV509877.1|DV509877
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211130112|gb|FL389065.1|FL389065
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|78112246|gb|DV530640.1|DV530640
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|37417263|gb|CF646284.1|CF646284
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211035296|gb|FL425638.1|FL425638
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|211137579|gb|FL389525.1|FL389525
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
EST: gi|149104177|gb|EE289611.2|EE289611
EST:     AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG                         GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG
genomic: AGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG

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), 48 (downstream exon)
Score: 303

GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 266

GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 279

GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 463

GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggc ... attggcgtagGAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGgtgtgttggctttcagtctttctgctccttttgccagttatagcagttctgacaaataagatgcaagttcatgtttcacaaactgctatatgtacaattt

- - - - - -  AGGAGA
- - - - - - - GGAGAA
- - - - - - - - - AAAGAA
- - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaataa