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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacgtaggcaaacagttccccctttttttttcccctcctccatccaatctatagaaacaaaagttagcaaaaaactgatttaatttctgttcctgcgtgcagAGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCGTGCACAGGCTGACGACGCCCAAGCCGCCGACGCCGAGCGCCGCTATCGG

Basic information

species Zea mays
transcript GRMZM2G175398_T04
intron # 3
splice site 3'
intron type U2

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|71443540|gb|DR824590.1|DR824590
EST:     GGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAG                         AGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCG
genomic: GGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAGgcacgtaggc ... ctgcgtgcagAGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCG
EST: gi|71319240|gb|DR796383.1|DR796383
EST:     GGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAG                         AGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCG
genomic: GGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAGgcacgtaggc ... ctgcgtgcagAGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCG
EST: gi|148958364|gb|EC904593.2|EC904593
EST:     GGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAG                         AGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCG
genomic: GGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAGgcacgtaggc ... ctgcgtgcagAGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCG

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: 26

CGGAGCTCGGCGCGCTGGGAGTCGTACACGCTGTTCCGCAAGTACGACGAGGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAGgcacgtaggc ... ctgcgtgcagAGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCGTGCACAGGCTGACGACGCCCAAGCCGCCGACGCCGAGCGCCGCTATCGG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 41

CGGAGCTCGGCGCGCTGGGAGTCGTACACGCTGTTCCGCAAGTACGACGAGGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAGgcacgtaggc ... ctgcgtgcagAGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCGTGCACAGGCTGACGACGCCCAAGCCGCCGACGCCGAGCGCCGCTATCGG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 23

CGGAGCTCGGCGCGCTGGGAGTCGTACACGCTGTTCCGCAAGTACGACGAGGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAGgcacgtaggc ... ctgcgtgcagAGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCGTGCACAGGCTGACGACGCCCAAGCCGCCGACGCCGAGCGCCGCTATCGG


Block sizes: 42 (upstream exon), 38 (downstream exon)
Score: 7

CGGAGCTCGGCGCGCTGGGAGTCGTACACGCTGTTCCGCAAGTACGACGAGGACATGGTCTACTTCCACCGCGTCGGCGCCCAGAAGCTCACCGAAACAGgcacgtaggc ... ctgcgtgcagAGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCGTGCACAGGCTGACGACGCCCAAGCCGCCGACGCCGAGCGCCGCTATCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatagaaacaaaagttagcaaaaaactgatttaatttctgttcctgcgtgcagAGTCGTTCCGGTCCATCAAGTACCAGCCGCGGTCGATGTCGGAGCGGATCGTGCACAGGCTGACGACGCCCAAGCCGCCGACGCCGAGCGCCGCTATCGG
                                    tttctgttcct  CT-rich tract
                     aaaaaactgatttaat  TA-rich tract