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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaattccatccatttatattcttttaatatgtgtttagcacagcaaacttccagtggtccattcctatttatattacttattatattcaaaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG

Basic information

species Zea mays
transcript GRMZM2G458549_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 5
-tgaattccatccatttatattcttttaatatgtgtttagcacagcaaacttccagtggtccattc--ctatttatattacttattatattcaaaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG
 | | ||| |   | || | |  ||| | | |   ||| |||      | |   |   || ||      | ||| |  || || ||  ||||||| | |||||||||||||||| |||||||| ||||  |||||||||||||||||||| |||||||| ||||||||||||
ctaagttcaa---acttctgtaatttcagtttcctttttgcattcattattcagaaaagttcaagagatttttttttctaatttttccattcaaatcatgcagAAAGAAGTTGCACAATTCACCTGTCAATCTGAGCGCCACATTGGAACACAATCTGGGGGCATGGATCAG
















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|76290432|gb|DV030000.1|DV030000
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTTCAAAG                         AAAGAAGTTTGCTCA-TTCACTTGTCTGTCTGAGCGCCACATTGGAACGCA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTT-GCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCA
EST: gi|50330093|gb|CO525219.1|CO525219
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|148960156|gb|EE153406.2|EE153406
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTG
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTG
EST: gi|32806294|gb|CD958528.1|CD958528
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|76283981|gb|DV023549.1|DV023549
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|89764289|gb|DY691150.1|DY691150
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|148955644|gb|EC901316.2|EC901316
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|148972046|gb|EE022887.2|EE022887
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|149071533|gb|EE159924.2|EE159924
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|76912626|gb|DV164825.1|DV164825
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|148965140|gb|EE015956.2|EE015956
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|78085244|gb|DV513637.1|DV513637
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGNCA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACG-CA
EST: gi|148991238|gb|EE032704.2|EE032704
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|148951727|gb|EC897480.2|EC897480
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|71318360|gb|DR795942.1|DR795942
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|148967123|gb|EE018297.2|EE018297
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
EST: gi|108824283|gb|EC278291.1|EC278291
EST:     GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG                         AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA
genomic: GTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAA

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), 49 (downstream exon)
Score: 113

GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

GCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAGgtattactta ... aaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacttccagtggtccattcctatttatattacttattatattcaaaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG
                attcctatttatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaattccatccatttatattcttttaatatgtgtttagcacagcaaacttccagtggtccattcctatttatattacttattatattcaaaccgtgcagAAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - ccatcca
- - - - - - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - -cagcaaa