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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgattcataatcctactctgtcgcattattatgtcaacgatactatcacacattatcatgtcatcaattatcacttcaacacaactttgccatcctaatcgtgtcaaatctttgttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAATTATGGTCTCGGTGGCATATGGGCTGGTCTTACTCTATTTATGAGTTTGC

Basic information

species Zea mays
transcript GRMZM5G890665_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G890665_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 10
gttctgattcataatcctactctgtcgcattattatgtcaacgatactatcacacattatcatgtcatcaattatcacttcaacacaactttgccatcctaatcgtgtcaa-atctttgttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAATTATGGTCTCGGTGGCATATGGGCTGGTCTTACTCTATTTATGAGTTTGC
                             ||   || || |   |  |||||      ||  | |  |   |||||| ||    | | ||    ||||||||||   | |  || ||| ||||||||||| |||||||||||  ||||||||  | | || ||  | || |||||||| | |||||| |||||| | |||||||| ||||||||||||||||||||||
----------------------------gttcagatttctat--tcttatcatgtcccattgtatagt---ttatcagtt----atagctgcagcatcctaatcacattagtatttttcttgtttcagTTATTTGCGGGAGCTATCTCATCAGCAGTACTGCTTGTGGCCGCTCCTAAGTTTGGTCTTGGTGGCGTCTGGGCTGGCCTTACTCTATTTATGAGTTTGC
















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|211305855|gb|FL435228.1|FL435228
EST:     ATGGGCTCTACTATGGTGTTTCTGACTTTGCTTATGCTGCATATTCCACG                         TTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAAT
genomic: ATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACGgttctgattc ... gttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAAT
EST: gi|9731973|gb|BE510725.1|BE510725
EST:     ATGGGCTCTACTATGGTGTTTCTGACTTTGCTTATGCTGCATATTCCACG                         TTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAAT
genomic: ATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACGgttctgattc ... gttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAAT
EST: gi|211236851|gb|FL081712.1|FL081712
EST:     CTGACTTTGCTTATGCTGCATATTCCACG                         TTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAAT
genomic: CTGACTTTGCCTATGCTGCATATTCCACGgttctgattc ... gttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAAT

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: 45 (upstream exon), 45 (downstream exon)
Score: 10

TTTGTCACCATTTCTCAGCCGGTGAATGCTATTGCATTCGTGGCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACGgttctgattc ... gttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAATTATGGTCTCGGTGGCATATGGGCTGGTCTTACTCTATTTATGAGTTTGC


Block sizes: 46 (upstream exon), 25 (downstream exon)
Score: 7

TTTGTCACCATTTCTCAGCCGGTGAATGCTATTGCATTCGTGGCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACGgttctgattc ... gttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAATTATGGTCTCGGTGGCATATGGGCTGGTCTTACTCTATTTATGAGTTTGC


Block sizes: 46 (upstream exon), 25 (downstream exon)
Score: 9

TTTGTCACCATTTCTCAGCCGGTGAATGCTATTGCATTCGTGGCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACGgttctgattc ... gttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAATTATGGTCTCGGTGGCATATGGGCTGGTCTTACTCTATTTATGAGTTTGC


Block sizes: 45 (upstream exon), 25 (downstream exon)
Score: 5

TTTGTCACCATTTCTCAGCCGGTGAATGCTATTGCATTCGTGGCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACGgttctgattc ... gttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAATTATGGTCTCGGTGGCATATGGGCTGGTCTTACTCTATTTATGAGTTTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcacttcaacacaactttgccatcctaatcgtgtcaaatctttgttgtttcagTTTTTTGCGGGAGCGGTCTCATCAATATTCCTACTATTAGCTGCTCCTAATTATGGTCTCGGTGGCATATGGGCTGGTCTTACTCTATTTATGAGTTTGC
                        tcctaat  putative branch site (score: 5)
                                        tctttgtt  putative PPT
                                     aaatcttt  TA-rich tract