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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttttgagacccttgcttgcttcacgtgtatgcagttatgcatcactctaccaagaaatttgaactgggcaatcagcaatcttagctacaagtttagtagcctctagtatgtatcactgaatgatattgcatttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAATTATTGGAACTGGTTTTGCATTTGGATTTCTTGTG

Basic information

species Zea mays
transcript GRMZM2G466281_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466281_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g02750.3 (Oryza sativa), 3'ss of exon 12
gtaagtcttttga---gacccttgcttgcttcacgtgtatgcagttatgcatcactctaccaa-----gaaatttgaactgggcaatcagcaatcttagctacaagtttagtagcctctagtatgtatcactgaatgatattgcatttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAATTATTGGAACTGGTTTTGCATTTGGATTTCTTGTG
|||   || || |    |  || | ||  ||   || |||    || |   ||  ||||  ||      |||||||| || | |||       |   || || | ||  |  | |||| || ||||  ||||||| ||| || ||||||||| |||||||||||| |||||||||||||||||||||| ||| |||||| | ||| ||||||||||||||||||||||||| |||||||||
gtatacctgttcacctaattctagtttagtt---gtatatatctttcttgttctttctattaatttattaaatttgagctagacaacagaagctagcagtta-aggtaaaaaatcctccagcatgt--cactgaaggatttttcatttttattcagGTCCTACCTATCTCCTTCAGATATAATGAGAAACCAGCCACATCTTCTAGTTATTGGAACTGGTTTTGCATTTGGCTTTCTTGTG
















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|149075136|gb|EE163629.2|EE163629
EST:     CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTG                         GTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAAT
genomic: CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTGgtaagtcttt ... ttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAAT
EST: gi|84980730|gb|DW531079.1|DW531079
EST:     CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTG                         GTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAAT
genomic: CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTGgtaagtcttt ... ttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAAT
EST: gi|24934262|gb|CA452480.1|CA452480
EST:     CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTG                         GTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAAT
genomic: CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTGgtaagtcttt ... ttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAAT

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: 46 (upstream exon), 48 (downstream exon)
Score: 232

CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTGgtaagtcttt ... ttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAATTATTGGAACTGGTTTTGCATTTGGATTTCTTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTGgtaagtcttt ... ttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAATTATTGGAACTGGTTTTGCATTTGGATTTCTTGTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 234

CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTGgtaagtcttt ... ttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAATTATTGGAACTGGTTTTGCATTTGGATTTCTTGTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 287

CTCTTTCCTTTTGGTTTGCTCTTGGCTGGAGTTCTTGTCTGgtaagtcttt ... ttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAATTATTGGAACTGGTTTTGCATTTGGATTTCTTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaagtttagtagcctctagtatgtatcactgaatgatattgcatttttatgcagGTCCTACCTTTCTCCTTCAGATATAATGAGAACCCAACCACATTTGCTAATTATTGGAACTGGTTTTGCATTTGGATTTCTTGTG
                                          cattttt  CT-rich tract
                                    atattgcatttttat  TA-rich tract