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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTTGCAGAACAACCAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatcaactgtgaaattcaatggtgctttatttgcatgttcattaccatatttcataacttgcttgcctctag

Basic information

species Zea mays
transcript GRMZM2G153393_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153393_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 8
GTATTTGCAGAACAACCAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatcaactgtgaaattcaatggtgctttatttgcatgttcattaccatatttcataactt-gcttgcctctag
 ||| |||||||||| |||||||||||| ||||||||||| | || ||||||||||||||   | ||| || |||||||  |  || | | |  |  |||||||||| || || ||||| || ||||| ||| |||| ||| |||
ATATCTGCAGAACAATCAATTTACTGGTTATATCAATGTCCTTGCTAATCTCCCCCTTGATGATCTgtaagaaatcaacc-tataagtaattaatattttatttgcacgtgcagtaccacatctcatatctttgctttcctatag

upper sequence: GRMZM2G153393_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 8
GTATTTGCAGAACAACCAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatcaactgtgaaattcaatggtgctttatttgcatgttcattaccatatttcataacttgcttgcctctag---------------------------------
|| |||||| ||||||||||||||||||| ||| |||||| | |||| ||| || |||||||| |||| |||  |    | | ||    ||||   ||  |    ||| | | || |  | ||||| ||      ||    | |                                 
GTTTTTGCAAAACAACCAATTTACTGGTAGTATTAATGTCCTTGCCAGTCTTCCTCTTGAAACATTgtaagtggtg---tatcaatcaaaatgcatctggagactcatatccctttctttttttcagaaaagatctgttatttggtcctttactatgttcatttttatgtttcttag
















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|71442375|gb|DR823425.1|DR823425
EST:     CAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTT                         GAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAA
genomic: CAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatc ... ttgcctctagGAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAA
EST: gi|211249064|gb|FL017587.1|FL017587
EST:     CAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTT                         GAATGTTGCGAACAACCATTTCACTGGTTGGGATTCCTAGTCAGCTTAAGA
genomic: CAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatc ... ttgcctctagGAATGTTGCGAACAACCATTTCACTGGTTGG-ATTCCTAGTCAGCTTAAGA
EST: gi|18659111|gb|BM500161.1|BM500161
EST:     CAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTT                         GAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAA
genomic: CAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatc ... ttgcctctagGAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAA
EST: gi|211249063|gb|FL017586.1|FL017586
EST:     CAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTT                         GAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAA
genomic: CAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatc ... ttgcctctagGAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAA

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), 49 (downstream exon)
Score: 154

GTATTTGCAGAACAACCAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatc ... ttgcctctagGAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAAGATAAACAGTCTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

GTATTTGCAGAACAACCAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatc ... ttgcctctagGAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAAGATAAACAGTCTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

GTATTTGCAGAACAACCAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatc ... ttgcctctagGAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAAGATAAACAGTCTACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 126

GTATTTGCAGAACAACCAATTTACTGGTAATATCAATGTCTTAGCCAATCTCCCCCTTGAAACTTTgtgagtaatc ... ttgcctctagGAATGTTGCGAACAACCATTTCACTGGTTGGATTCCTAGTCAGCTTAAGAAGATAAACAGTCTACA