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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtggcgctccactccccgcgccccagcgcttcgaatcccgaccgcagctcacgcccctccttttttgcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTAAGCGGGCGGCGGACGACCGCGCCCCCCCGGCCCCTACTCCCGAG

Basic information

species Zea mays
transcript GRMZM2G048455_T01
intron # 1
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|148971968|gb|EE022765.2|EE022765
EST:     TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
EST: gi|76925341|gb|DV170391.1|DV170391
EST:     TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
EST: gi|148944537|gb|EC889659.2|EC889659
EST:     TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
EST: gi|148976341|gb|EE025924.2|EE025924
EST:     TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
EST: gi|76287945|gb|DV027513.1|DV027513
EST:     TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
EST: gi|88756056|gb|DY540197.1|DY540197
EST:     TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
EST: gi|71757469|gb|DR955406.1|DR955406
EST:     TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
EST: gi|76012144|gb|DT939314.1|DT939314
EST:     TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
EST: gi|78109405|gb|DV527821.1|DV527821
EST:     TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: TACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
EST: gi|31353430|gb|CD437787.1|CD437787
EST:     ACGGCGGCGGTCC-GTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACG                         TGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA
genomic: ACGGCGGCGG-CCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTA

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), 47 (downstream exon)
Score: 66

CCCCAACATCCCCCCTCCCCGCTCCGCTCCACGCACGGCTCCAGATCTGCTACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTAAGCGGGCGGCGGACGACCGCGCCCCCCCGGCCCCTACTCCCGAG


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 22

CCCCAACATCCCCCCTCCCCGCTCCGCTCCACGCACGGCTCCAGATCTGCTACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTAAGCGGGCGGCGGACGACCGCGCCCCCCCGGCCCCTACTCCCGAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 25

CCCCAACATCCCCCCTCCCCGCTCCGCTCCACGCACGGCTCCAGATCTGCTACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTAAGCGGGCGGCGGACGACCGCGCCCCCCCGGCCCCTACTCCCGAG


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

CCCCAACATCCCCCCTCCCCGCTCCGCTCCACGCACGGCTCCAGATCTGCTACGGCGGCGGCCGGTGGACGCCGCGCCGCGCGTGCCGGAGGCGGTGACGgtgggtggcg ... gcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTAAGCGGGCGGCGGACGACCGCGCCCCCCCGGCCCCTACTCCCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccagcgcttcgaatcccgaccgcagctcacgcccctccttttttgcccgtgcagTGAGCGGCGGATCCTGCCCGGCCGTGCCATCCTGGCGACGATGACAGCGTAAGCGGGCGGCGGACGACCGCGCCCCCCCGGCCCCTACTCCCGAG
                        agctcac  putative branch site (score: 47)
                          ctcacgcccctccttt  CT-rich tract
                                       tttttt  TA-rich tract