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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCAGAAACAGGTGTTTCCCTTGCATATACTGTCCGTGCATTGGATGCAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgatattcactgtcttcctagtttgatatgtcatcttgacgatgcaaagttatataacaaggcatcccttcattttagaggaattagaattcact...

Basic information

species Zea mays
transcript GRMZM2G019437_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019437_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g49330.1 (Oryza sativa), 5'ss of exon 5
TGTTGCAGAAACAGGTGTTTCCCTTGCATATACTGTCCGTGCATTGGATGCAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgatattcactgtcttcctagtttgatatgtcatcttgacgatgcaaagttatataaca-aggcatcccttcattttagaggaattagaattcact
||||| |||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||| | ||||| |||| |||| ||||| | |||||||||||||| |  | |||||||| || |||| || | ||||||||||  |  ||| || || |||| | |    || |   || |  | || || |  |    
TGTTGAAGAAACAGGTGTTTCCCTTGCATATACTGTCCGTGCCTTGGATGCGGGTCCAGTTATTGCTTCTGAAAAGTTTGCTGTAGATGAGTATATTAAGgtaggtggttctaactgtcttgctggttttat-tatcatcttgacagtttaaatttctagaacagaagtcaaccattgcttgaatgaaaatatacatgggc
















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|31360881|gb|CD445238.1|CD445238
EST:     CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAG                         GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
genomic: CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
EST: gi|67022687|gb|CO451436.1|CO451436
EST:     CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAG                         GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
genomic: CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
EST: gi|71420934|gb|DR805240.1|DR805240
EST:     CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAG                         GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
genomic: CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
EST: gi|149076153|gb|EE164742.2|EE164742
EST:     CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAG                         GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
genomic: CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
EST: gi|67023553|gb|CO452302.1|CO452302
EST:     CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAG                         GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
genomic: CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
EST: gi|50332369|gb|CO527495.1|CO527495
EST:     CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAG                         GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
genomic: CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
EST: gi|76289469|gb|DV029037.1|DV029037
EST:     CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAG                         GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
genomic: CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
EST: gi|148952757|gb|EC898739.2|EC898739
EST:     CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAG                         GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
genomic: CAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG
EST: gi|71420929|gb|DR805239.1|DR805239
EST:     AATGTATTAAG                         ACACCAGAGCTACTTTCTATGCTGTTTCATTTAG
genomic: AATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG

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), 46 (downstream exon)
Score: 39

TGTTGCAGAAACAGGTGTTTCCCTTGCATATACTGTCCGTGCATTGGATGCAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 30

TGTTGCAGAAACAGGTGTTTCCCTTGCATATACTGTCCGTGCATTGGATGCAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG


Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 12

TGTTGCAGAAACAGGTGTTTCCCTTGCATATACTGTCCGTGCATTGGATGCAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG


Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 19

TGTTGCAGAAACAGGTGTTTCCCTTGCATATACTGTCCGTGCATTGGATGCAGGTCCAGTGATTGCGTGTGAAAGGTTTTCTGTTGATGAATGTATTAAGgtaggtgata ... ttgtttgcagGCACCAGAGCTACTTTCTATGCTGTTTCATTTAG