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'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatgatacacaaactctcctgtgcgttcgagagaaaaaatgccttctgcattcactttgagatatgtggtgagtttcaatttctatttaaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA

Basic information

species Zea mays
transcript GRMZM2G032628_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 15
ataatgatacacaaactctcctgtgcgttcgagagaaaaaatgccttctgcattcact--ttgagatatgtggt----gagtttcaatttctatttaaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA
 | | | |    |   | |  |  |     | || | |   |   || || || |  |  |||| | |||||||    |||||||||||| ||||| ||   ||||||||||||||||| |||||||||||||||||||||||||||||||||| || || ||||||| |||||||||||| ||||||||||||||||||||||||
-tca-gctgtttagcttttatttagaaactgggaaagattgt-tattttgtatcctttaattgaaagatgtggtgccagagtttcaatttttattttac---acagGCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAACAGAAGGTGGTCAGAGAAGTGTGTTACTTATGCTGAAAGTCATGATCAA

upper sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 15
ataatgatacacaaactctcctgtgcgttcgagagaaaaaatgccttctgcattcactttgagata----tgtggtgagtttcaatt-tctatttaaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA
        |    | |||       |  |       |    | |  | ||||   | | ||| |        |||    |||||    | | |||    |   ||| | |  ||||||   ||||| |||||||||||  | |||||| | ||||| || |||||| | || || |||||| ||||||||||||||||||| || 
-----atcatttcatctccaacaaccactgtcattcattcttactgtttgcaagtagtgtgaaaagaaaccatgggtgatttcagcagtgtctttttttgtgtagGAAGAACGATGAAGACTGGAAAATGGGTGATATCATCCACACATTAACAAACAGAAGGTGGCTGGAAAAATGTGTAGCTTATGCTGAAAGTCATGACCAG

upper sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 15
ataatgatacacaaactctcctgtgcgttcgagagaaaaaatgccttctgcattcactttgagatatgtggtgagtttcaatttc-----tatttaaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA
        |    | |||   ||  |  |            | |  | || |   | | ||| | |     | |  |  ||||||     | |      |   ||| | | |||||||   ||||| |||||||||||||| |||||| | ||||| || |||||| | || || |||||| ||||||||||||||||||| || 
----catcatttcatctccaatgaccactgtcattcgttcttactgtttgtaagtagtgtgaaa-agaaaatcatgtgtaatttcagcggtgtccttttgtgtagGAAGAATGATGAAGACTGGAAAATGGGTGATATTGTCCACACATTAACAAACAGAAGGTGGCTGGAAAAATGTGTAGCTTATGCTGAAAGTCATGACCAG

upper sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 15
-ataatgatacacaaactctcctgtgcgttcgagagaaaaaatgccttctgcattcactttgagatatgtggtgagtttcaatttctatttaaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA
   | || |      | | || | |  |||| |            |||    |||     ||| ||| |||      |    |   | ||   | |   ||| | || ||||||   ||| | ||||| || ||  |  ||||||| || || || ||||||| |||||||||| |  |||||||||||||||| ||||||
gtgagtgttttctgcattttcttttaagttccatctg--------ctttaatatttgg--tgaaataagtgtcttactctcctccatgttatgctgtgaagGAAGAGAGATGAAGACTGGCAAATGGGCGACATCATTTACACACTTACCAACAGAAGGTGGTCAGAGAAGTGTATCTCTTATGCTGAAAGTCACGATCAA

upper sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 15
ataatgatacacaaactctcctgtgcgttcgagagaaaaaatgccttctgcattcactttgagatat-gtggtgagtttca-atttctatttaaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA
    || || || |  ||      | |||        | | |   ||     ||  |||   | |||  |  |   ||||| ||    ||   |     |||| ||  |||||||  |||||| |||||||| ||| | ||||| || || ||||| |||||||| || || |||||  ||||||||||||||||||| |||
--tttggtataccaggtcaagaaagagttgttttaccatagtttattaattttttccttcatgttattataattcatttcacatgcaaatgctatgatgcagGAAACCTGATGAATATTGGAAAATGGGTGACATTATTCACACGCTCACCAATAGAAGGTGGTTGGAAAAATGTGTTGCTTATGCTGAAAGTCATGACCAA

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|67017922|gb|CO446671.1|CO446671
EST:     ACTATCGGNTGCATATGGACTGCCGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: ACTATCGGATGCATATGG-CTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|6578060|gb|AW244197.1|AW244197
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|31360518|gb|CD444875.1|CD444875
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|32838173|gb|CD977851.1|CD977851
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|67032923|gb|CO461672.1|CO461672
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|31361510|gb|CD445867.1|CD445867
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|67034885|gb|CO463418.1|CO463418
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|67023243|gb|CO451992.1|CO451992
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|91873181|gb|EB403138.1|EB403138
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|31357480|gb|CD441837.1|CD441837
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|31360077|gb|CD444434.1|CD444434
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|67011365|gb|CO440114.1|CO440114
EST:     GGCTGACATTTGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|24765115|gb|CA400276.1|CA400276
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|67018905|gb|CO447654.1|CO447654
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|108953879|gb|EC364910.1|EC364910
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
EST: gi|31355884|gb|CD440241.1|CD440241
EST:     GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAA                         GCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA
genomic: GACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAA

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: 48 (upstream exon), 45 (downstream exon)
Score: 66

GTGGAATGCCTACATTTGCCCTTCCTGTTCACGATGGTGGGGTAGGTTTTGACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA


Block sizes: 34 (upstream exon), 45 (downstream exon)
Score: 11

GTGGAATGCCTACATTTGCCCTTCCTGTTCACGATGGTGGGGTAGGTTTTGACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 14

GTGGAATGCCTACATTTGCCCTTCCTGTTCACGATGGTGGGGTAGGTTTTGACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 291

GTGGAATGCCTACATTTGCCCTTCCTGTTCACGATGGTGGGGTAGGTTTTGACTATCGGATGCATATGGCTGTGGCTGACAAATGGATTGACCTTCTCAAgtaagtgttt ... aaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcattcactttgagatatgtggtgagtttcaatttctatttaaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA
                                         atttaac  putative branch site (score: 291)
                              tttcaatttctattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatgatacacaaactctcctgtgcgttcgagagaaaaaatgccttctgcattcactttgagatatgtggtgagtttcaatttctatttaaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - -gatacac
- - - - - - - - - -cctgtgc
- - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - cttctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg