Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcttgtgttgataatttgataactgtctttccgaatatatcaagttacttgttgcgataaagggaggctaactttttcactcgtgatcgattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTCTTTATCAATTGTTTACGGGGGACAGGATATTGGCTAGGTATCTCTGTAG

Basic information

species Zea mays
transcript GRMZM2G316635_T01
intron # 6
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|4775892|gb|AI664895.1|AI664895
EST:     CTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAG                         GAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC
genomic: CTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAGgtgtgttctt ... gattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC
EST: gi|78026568|gb|DV494955.1|DV494955
EST:     CTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAG                         GAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC
genomic: CTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAGgtgtgttctt ... gattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC
EST: gi|21331195|gb|BQ486576.1|BQ486576
EST:     CTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAG                         GAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC
genomic: CTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAGgtgtgttctt ... gattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC
EST: gi|4624195|gb|AI615028.1|AI615028
EST:     AATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAG                         GAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC
genomic: AATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAGgtgtgttctt ... gattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC
EST: gi|12969862|gb|BG266694.1|BG266694
EST:     CTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAG                         GAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC
genomic: CTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAGgtgtgttctt ... gattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 83

CAGGAAGGCAACCCTTTGTGTCCATCCAGATAAAGTGCAGCAAAGAGGTGCTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAGgtgtgttctt ... gattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTCTTTATCAATTGTTTACGGGGGACAGGATATTGGCTAGGTATCTCTGTAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 23

CAGGAAGGCAACCCTTTGTGTCCATCCAGATAAAGTGCAGCAAAGAGGTGCTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAGgtgtgttctt ... gattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTCTTTATCAATTGTTTACGGGGGACAGGATATTGGCTAGGTATCTCTGTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 47

CAGGAAGGCAACCCTTTGTGTCCATCCAGATAAAGTGCAGCAAAGAGGTGCTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAGgtgtgttctt ... gattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTCTTTATCAATTGTTTACGGGGGACAGGATATTGGCTAGGTATCTCTGTAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 27

CAGGAAGGCAACCCTTTGTGTCCATCCAGATAAAGTGCAGCAAAGAGGTGCTACAATCAGACAGAAATACATTTGTGAGAAGGTGTTTGATCTTCTTAAGgtgtgttctt ... gattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTCTTTATCAATTGTTTACGGGGGACAGGATATTGGCTAGGTATCTCTGTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacttgttgcgataaagggaggctaactttttcactcgtgatcgattgtgcagGAGGCTTGGAATAAGTACAATTCTGAAGAGCGCTAGTGGGATAGGTGGTTCTTTATCAATTGTTTACGGGGGACAGGATATTGGCTAGGTATCTCTGTAG
                      ggctaac  putative branch site (score: 27)
                         taacttttt  TA-rich tract