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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctaaaccccaaatcttgtttgatttctattgctagttttgcgtacttgaaaaaaagggactgacaggttcaatacttgttagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATGGTAGATATCAACATGGTATCCGCAATACTGTTTGTGGTGATTGCATCAT

Basic information

species Zea mays
transcript GRMZM2G096343_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 5
gttctaaaccccaaatcttgtttgatttctattgctagttttgcgtacttgaaaaaaagggactgacaggttcaatacttgt-tagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATGGTAGATATCAACATGGTATCCGCAATACTGTTTGTGGTGATTGCATCAT
||||| |||    || ||| ||||| |  | ||     |||||  | |||||||| |  | ||| ||||         || | |||||||| | ||||    ||| |||||| ||| |||| ||||||||||| ||||||||||||||||||  ||| |||||||||||||| || |||||||| |
gttctgaaca--gaagcttatttgactattgttctggattttgtttgcttgaaaaga--gaactaacagtcatttggtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATGGTAGATATCAACATGACATCGGCAATACTGTTTGTTGTTATTGCATCTT
















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|211335511|gb|FL455439.1|FL455439
EST:     CAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAG                         GATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATG
genomic: CAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAGgttctaaacc ... tacttgttagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATG
EST: gi|211297692|gb|FL447045.1|FL447045
EST:     CAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAG                         GATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATG
genomic: CAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAGgttctaaacc ... tacttgttagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATG
EST: gi|71422117|gb|DR805619.1|DR805619
EST:     CAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAG                         GATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATG
genomic: CAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAGgttctaaacc ... tacttgttagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATG

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), 49 (downstream exon)
Score: 41

GTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAGgttctaaacc ... tacttgttagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATGGTAGATATCAACATGGTATCCGCAATACTGTTTGTGGTGATTGCATCAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 125

GTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAGgttctaaacc ... tacttgttagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATGGTAGATATCAACATGGTATCCGCAATACTGTTTGTGGTGATTGCATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAGgttctaaacc ... tacttgttagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATGGTAGATATCAACATGGTATCCGCAATACTGTTTGTGGTGATTGCATCAT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 59

GTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAGgttctaaacc ... tacttgttagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATGGTAGATATCAACATGGTATCCGCAATACTGTTTGTGGTGATTGCATCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgctagttttgcgtacttgaaaaaaagggactgacaggttcaatacttgttagGATGGTCGTGAAGTAGCACCAAACTTTGAGCCTGGAGGTTCTAGTGGTATGGTAGATATCAACATGGTATCCGCAATACTGTTTGTGGTGATTGCATCAT
                              gactgac  putative branch site (score: 59)
                  ttgaaaaaaa  TA-rich tract