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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgactgccaatgcatactattagaaatgcttcattggtagatttgaactactgttagcatgactgaattgtttggttggcatag

Basic information

species Zea mays
transcript GRMZM2G154165_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154165_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G01270.1 (Glycine max), 5'ss of exon 4
GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgactgccaatgcatactattagaaatgcttcattggtagatttgaactactgttagcatgac--tgaattgtttggttggcatag------------------------------------------------------------------
|||||| || || ||||| |||||||| |||||||||||||||||||| | || || || || |||||||||| | || | || | || | | | || | ||| | | ||| | | | ||| | ||||
GTATCCCCTCGGTCGTGTAATTGGTGGGACTGTCTATCCTGGTTTGACGTTGACAGCAGGCACCTTATGGTGgtaggcatttgaaacacagtaatgttggttgtcatatgctgtgatttttctcttcattttatactaatattaaatatccatgcaagcatttgttttgaagtttatcagtttatctaaggtggttgatatttttggaccattcccttcttggtttcag

upper sequence: GRMZM2G154165_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G08410.1 (Glycine max), 5'ss of exon 4
GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgactgccaatgcatactattag-----aaatgcttcattggtagatttgaactactgttagcatgactgaattgtttggttggca-tag--------------------------------------------------------
|||||| ||||| ||||| |||||||| |||||||||||||||||||| | || || || || ||||| |||| | || | || | || | | ||||| | | || | | | || | | | ||| | ||| | |
GTATCCCCTTGGTCGTGTAATTGGTGGGACTGTCTATCCTGGTTTGACCTTGACAGCAGGCACCTTATGGCGgtaggcatttgaaacacagtaatgttggttgtcatatgctgtgatttttctcttcattttatagtaataatattaaatatccatgcaagcaattgttttgaagtttatctaaggtgtttggtatttttggacctttcccttctggtttcag

upper sequence: GRMZM2G154165_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 5'ss of exon 4
GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgactg---ccaatgcatactattag----aaatgcttcat--tggtagatttga-actactgttagcatgactgaattg--tttggttggcatag----------------------------------------------------------------------------------------------
|||||||||||| ||||| |||||||||||||| || || || ||||| | || || || | |||||||||| || || |||| | || | | | || || ||| |||| | | || || || | || |||| | |||| |
GTATCCTCTTGGTCGTGTGATTGGTGGCACTGTTTACCCAGGATTGACCTTAACAGCAGGCTCCATATGGTGgtgggtatttgagattggtgcaacttgtttgttgcaggagattaatgccattagttttgttatttctttttgctt--ctagattgagtacagttgctcttaatcagtttccatatataatgagacattggaaatagtacctgtgaatgagtcctgtggcagctaatgattatgggccaatactttctgatggcag

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|71447978|gb|DR829028.1|DR829028
EST:     GGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG                         GTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATT
genomic: GGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgact ... gttggcatagGTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATT
EST: gi|93015443|gb|EB640963.1|EB640963
EST:     GGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG                         GTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATT
genomic: GGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgact ... gttggcatagGTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATT
EST: gi|71447977|gb|DR829027.1|DR829027
EST:     GGAGGGACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG                         GTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATT
genomic: GGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgact ... gttggcatagGTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATT

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: 156

GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgact ... gttggcatagGTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATTCACTGCTCCAGTTTTCTCAGTCAATGCGTCCTGGGCAACTTACCTATTA


Block sizes: 48 (upstream exon), 31 (downstream exon)
Score: 10

GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgact ... gttggcatagGTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATTCACTGCTCCAGTTTTCTCAGTCAATGCGTCCTGGGCAACTTACCTATTA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 14

GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgact ... gttggcatagGTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATTCACTGCTCCAGTTTTCTCAGTCAATGCGTCCTGGGCAACTTACCTATTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 50

GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTGgtatgtgact ... gttggcatagGTTGTTGAATTCCCTTAACATCCCATTGTCGGTGGAGACTGTCTGTGTATTCACTGCTCCAGTTTTCTCAGTCAATGCGTCCTGGGCAACTTACCTATTA