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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatggatctacctttgtaccaggttatgcagtacactttgtcatactcagatacttattttgaatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGTGGATCATCTCAGCAATCACCACAGCAACCTCACATTTCATATTTCTCCA

Basic information

species Zea mays
transcript GRMZM2G065130_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065130_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 31
gtgatggatctacctt-----tgtaccaggttatgcagtacactttgtcatactcagatacttatt--ttgaatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGTGGATCATCTCAGCAATCACCACAGCAACCTCACATTTCATATTTCTCCA
||||||  |||| |||     ||||| || || ||   | || |||   |||||    || ||| |  | || ||   |||||||||||||||| ||||||||||||| || | ||||| |||||| ||||||||   |||||| | ||| |||| ||||   | |||||||||||| | |
gtgatgattctagcttgtaattgtactagatt-tgttcttcagttttctatacttgagtatttaatgttcgagtcaaacagGAACTTGCTGTTAAACACTCTCTAGTCCCCAATCAGATTGTTGCTACTGGTGGAGTGTCTCAGAAGTCATCACAACAACTCAAAATTTCATATTTCCCAA
















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|211221898|gb|FL409207.1|FL409207
EST:     GTCTGCTGAAGGGGGATGATATCTCTGAACGCTTCTTCCGTATTCTCACG                         GAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAAATCGTTGCTCCTGGT
genomic: GTCTGCTGAAGGGGGATGATATCTCTGAACGCTTCTTCCGTATTCTCACGgtgatggatc ... aatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGT
EST: gi|74243504|gb|DT651418.1|DT651418
EST:     TTCTTCCGTATTCTCACG                         GAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGT
genomic: TTCTTCCGTATTCTCACGgtgatggatc ... aatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGT
EST: gi|211122374|gb|FL379873.1|FL379873
EST:     GTCTGCTGAAGGGGGATGATATCTCTGAACGCTTCTTCCGTATTCTCACG                         GAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAAATCNGTTGCTCCTGG
genomic: GTCTGCTGAAGGGGGATGATATCTCTGAACGCTTCTTCCGTATTCTCACGgtgatggatc ... aatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATC-GTTGCTCCTGG

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: 518

TGCTAGTGATGCGGCATACACTCGTTTTGTCACACAGTTGCAGCAAGATGGTCTGCTGAAGGGGGATGATATCTCTGAACGCTTCTTCCGTATTCTCACGgtgatggatc ... aatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGTGGATCATCTCAGCAATCACCACAGCAACCTCACATTTCATATTTCTCCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 215

TGCTAGTGATGCGGCATACACTCGTTTTGTCACACAGTTGCAGCAAGATGGTCTGCTGAAGGGGGATGATATCTCTGAACGCTTCTTCCGTATTCTCACGgtgatggatc ... aatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGTGGATCATCTCAGCAATCACCACAGCAACCTCACATTTCATATTTCTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 253

TGCTAGTGATGCGGCATACACTCGTTTTGTCACACAGTTGCAGCAAGATGGTCTGCTGAAGGGGGATGATATCTCTGAACGCTTCTTCCGTATTCTCACGgtgatggatc ... aatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGTGGATCATCTCAGCAATCACCACAGCAACCTCACATTTCATATTTCTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

TGCTAGTGATGCGGCATACACTCGTTTTGTCACACAGTTGCAGCAAGATGGTCTGCTGAAGGGGGATGATATCTCTGAACGCTTCTTCCGTATTCTCACGgtgatggatc ... aatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGTGGATCATCTCAGCAATCACCACAGCAACCTCACATTTCATATTTCTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaggttatgcagtacactttgtcatactcagatacttattttgaatcgttcagGAACTTGCTGTTACACACTCTCTAGTCTCCGAGCAGATCGTTGCTCCTGGTGGATCATCTCAGCAATCACCACAGCAACCTCACATTTCATATTTCTCCA
                                 atacttattttgaat  TA-rich tract