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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgagcaccatgtgttttggtgaattatttgtcctctatgtagttctgtaaagtgatgttgcagtgataattctttgcatctcttcttgtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTTGGCTGCAAGGAGTCCTGGTTTGGGCAACGTTGACAATCTCCATGAG

Basic information

species Zea mays
transcript GRMZM5G868168_T04
intron # 1
splice site 3'
intron type U2

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|50324151|gb|CO519277.1|CO519277
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|149004790|gb|EE039293.2|EE039293
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|149078033|gb|EE166771.2|EE166771
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|78120174|gb|DV538558.1|DV538558
EST:     CTTTTCCACTCGCCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|211380394|gb|FK976874.1|FK976874
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|31350150|gb|CD434507.1|CD434507
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|33467141|gb|CF244190.1|CF244190
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|78103984|gb|DV522402.1|DV522402
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|154130463|gb|EC872173.2|EC872173
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|76931706|gb|DV172823.1|DV172823
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|148986921|gb|EE030732.2|EE030732
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|149080766|gb|EE169831.2|EE169831
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|211380395|gb|FK976875.1|FK976875
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
EST: gi|91048130|gb|EB158548.1|EB158548
EST:     CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAG                         GATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT
genomic: CTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTT

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), 36 (downstream exon)
Score: 19

CCATCCCCGCCGCTCTCCGCCACCCGCACCTCCCCGCCGATGGAGGACTTCTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTTGGCTGCAAGGAGTCCTGGTTTGGGCAACGTTGACAATCTCCATGAG


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 52

CCATCCCCGCCGCTCTCCGCCACCCGCACCTCCCCGCCGATGGAGGACTTCTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTTGGCTGCAAGGAGTCCTGGTTTGGGCAACGTTGACAATCTCCATGAG


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 33

CCATCCCCGCCGCTCTCCGCCACCCGCACCTCCCCGCCGATGGAGGACTTCTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTTGGCTGCAAGGAGTCCTGGTTTGGGCAACGTTGACAATCTCCATGAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 45

CCATCCCCGCCGCTCTCCGCCACCCGCACCTCCCCGCCGATGGAGGACTTCTTTTCCACTCGTCCGGCGACCCAACCGCGCGCTCCTCGCTCTCGTTCAGgcaaaacttt ... gtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTTGGCTGCAAGGAGTCCTGGTTTGGGCAACGTTGACAATCTCCATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtaaagtgatgttgcagtgataattctttgcatctcttcttgtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTTGGCTGCAAGGAGTCCTGGTTTGGGCAACGTTGACAATCTCCATGAG
                           ttctttgcatctcttc  CT-rich tract
                       ataattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatgagcaccatgtgttttggtgaattatttgtcctctatgtagttctgtaaagtgatgttgcagtgataattctttgcatctcttcttgtttaagcagGATAGGAGACATGACAATGAGAAGGTGTCAGACAGGTCCTGGTCCTGTTTTGGCTGCAAGGAGTCCTGGTTTGGGCAACGTTGACAATCTCCATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - -agcacca
- - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca