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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcgcactctgtgggggtagtttattgcattttactttagactacaaaacaacacacatttgaaaattactgtttcatgcttgtggtgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG

Basic information

species Zea mays
transcript GRMZM2G063492_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 8
gtctgcgcactctgtgggggtagtttattgcattttactttagactacaaaacaacacacatttgaaaattactgtttcatgcttgtggtgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG
|||||| | || ||||         |    ||   || |||    |  |         | || ||||||| | |||  || ||||||| ||   |||||||| |||||||| ||||||||| ||||||||||||||||||| ||||||||||| ||| | || |||
gtctgctc-ctatgtgatttagtcatgccacagagtagtttgtttttta------tgtagatatgaaaatcattgtggcaagcttgtgatgttatgcagACACTCAACTGACAGAGAAGTTGCTATCATGATACTCATGGCGTACCTTTCATATATGCTGTCGATG

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G02560.1 (Glycine max), 3'ss of exon 6
gtctgcgcactctgtgggggtagtttattgcattttactttagactacaaaa-----caacacacatttgaaaattactgtttcatgcttgtggtgacgtg---cagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG
||     |    |          || | |    || ||   | || |  |||     ||  ||||  |||   |||| |   | || | | |  ||||      ||| ||||| || ||  | || ||| || ||||| |||||||||||||||||||||| ||| ||||    
gttaattctaaattccattacttttgaatatgcttaaccaca-acaatgaaatatcccagtacactgttggccattattccctaattcctttactgacaaatcccagGCATTCTACAGACCGTGAGGTTGCTCTCATGGTACTCATGGCATACCTTTCATATATGCTATCTGAA
















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|18963600|gb|BM660526.1|BM660526
EST:     ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGCTTTGCCAG                         ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTC
genomic: ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGCTTTGCCAGgtctgcgcac ... tgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTC
EST: gi|71311178|gb|DR791899.1|DR791899
EST:     ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGTTTTGCCAG                         ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTC
genomic: ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGCTTTGCCAGgtctgcgcac ... tgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTC
EST: gi|89106454|gb|DY576671.1|DY576671
EST:     AGTGCATACATTATCAAGAAGCTCTGCTTTGCCAG                         ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTC
genomic: AGTGCATACATTATCAAGAAGCTCTGCTTTGCCAGgtctgcgcac ... tgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTC
EST: gi|67026824|gb|CO455573.1|CO455573
EST:     ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGCTTTGCCAG                         ACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTC
genomic: ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGCTTTGCCAGgtctgcgcac ... tgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 89

ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGCTTTGCCAGgtctgcgcac ... tgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 253

ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGCTTTGCCAGgtctgcgcac ... tgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 254

ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGCTTTGCCAGgtctgcgcac ... tgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 85

ACCGGGTTGCTTAGTGCATACATTATCAAGAAGCTCTGCTTTGCCAGgtctgcgcac ... tgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacaaaacaacacacatttgaaaattactgtttcatgcttgtggtgacgtgcagACATTCAACTGATAGAGAAGTTTCTATCATGATACTCATGGCATACCTTTCATACATGATATCAATG
              acatttgaaaatta  TA-rich tract