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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattcttcctcatcttatattattattaccgaggaacaatgctttgcattttatacctagaatagctcttactgacatgttgaaccacttgaagcctcctagtaggcttaattccatgtgtatcctatcacctcattaagttggtgctgacttgtttgtgttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATATTGCAGTTATCAAATGACCTAGGAGTTCAATGATAAGATCGTGATGACA

Basic information

species Zea mays
transcript GRMZM2G459642_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G459642_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 6
-----------gttattcttcctcatctt-------atatt---attattac-cgaggaacaatgctttgcattt-tatacctagaatagctcttactgacatgttgaaccacttgaagcctcctagtaggcttaattccatgtgtatcctatcacctcattaagttggtgctgac---ttgtttgtgttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATATTGCAGTTATCAAATGACCTAGGAGTTCAATGATAAGATCGTGATGACA
            || | ||  |||||  |       | |||   | ||||||  ||    ||    | |||||   | || ||||| ||| |  |  |  || |        ||| |||  || ||| ||| || ||| ||||  ||||  ||  |   |||| || ||| |||||   || |||   || |||||||||||||||||| ||||| |||||||||||||||||||| |||||||||||| ||||||| ||||| || ||||||||||||| || |        ||  |
gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggt-gcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
















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|60346719|gb|DN213692.1|DN213692
EST:     CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|60399844|gb|DN232654.1|DN232654
EST:     CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|60353564|gb|DN220537.1|DN220537
EST:     AAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: AAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|211383655|gb|FL455017.1|FL455017
EST:     AGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: AGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|33091264|gb|CF051258.1|CF051258
EST:     CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|60344784|gb|DN211757.1|DN211757
EST:     CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|6056553|gb|AW090943.1|AW090943
EST:     CAGAGATATACCAACGGATGCTTNAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTT
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTT
EST: gi|60401545|gb|DN234352.1|DN234352
EST:     ATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: ATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA

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: 44 (upstream exon), 48 (downstream exon)
Score: 89

AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATATTGCAGTTATCAAATGACCTAGGAGTTCAATGATAAGATCGTGATGACA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 81

AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATATTGCAGTTATCAAATGACCTAGGAGTTCAATGATAAGATCGTGATGACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 74

AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATATTGCAGTTATCAAATGACCTAGGAGTTCAATGATAAGATCGTGATGACA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 55

AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATATTGCAGTTATCAAATGACCTAGGAGTTCAATGATAAGATCGTGATGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgtatcctatcacctcattaagttggtgctgacttgtttgtgttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATATTGCAGTTATCAAATGACCTAGGAGTTCAATGATAAGATCGTGATGACA
                             tgctgac  putative branch site (score: 55)
                   attaagtt  TA-rich tract