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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcgtgtgacttttcacttcattgatggtattcagtatttcttatccttcagatatgttgcttacataatgcctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGACCACCAA

Basic information

species Zea mays
transcript GRMZM2G165817_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165817_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 5
gcgtgtgactt-ttcacttcattgatggtattcagtatttcttatccttcagatatgttgcttacataatgcctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGACCACCAA
| ||||   ||  |||||| || | | |||  || | |||   |  ||    ||   |||     |||||      ||||||||||||||||||||||| || ||||| ||||||||||| ||||| || |||||||| ||||||||||||||||||||||| || |||
gtgtgtcgtttgctcacttaataggtagtagcca-tcttttacaaactaattattctttgtactgataatttggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTGATTAGGGAAATGTTTGGCTATGCACGTGATCATCAA
















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|60400478|gb|DN233285.1|DN233285
EST:     CCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAGgcgtgtgact ... ctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|211475160|gb|FL103093.1|FL103093
EST:     CCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAGgcgtgtgact ... ctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|95107783|gb|EB740012.1|EB740012
EST:     CCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATTATCGACAAA-ACCATTGGAGAAAGTGCTCGTTT
genomic: CCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAGgcgtgtgact ... ctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATAC-ATTGGAGAAAGTGCTCGTTT
EST: gi|148950536|gb|EC896111.2|EC896111
EST:     CCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAGgcgtgtgact ... ctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTG

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: 48 (upstream exon), 49 (downstream exon)
Score: 246

GGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAGgcgtgtgact ... ctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGACCACCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 161

GGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAGgcgtgtgact ... ctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGACCACCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

GGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAGgcgtgtgact ... ctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGACCACCAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 155

GGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAGgcgtgtgact ... ctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGACCACCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattcagtatttcttatccttcagatatgttgcttacataatgcctgaaaacagATTGTTTCAAGTGCTATTATCGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGACCACCAA
                               tgcttac  putative branch site (score: 155)
        tatttcttat  TA-rich tract