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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgtcctagctagctcttgctcttgctcttgggagcaaggggagtacgtacgtatcagcaaccgatcgactgcttgctcctcacacctcgatggatcgttcgtgcgtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCGGCGCCGCCAAGGGGCTGGCTTTCCTCCACGCCGCCAACACGCCCGTCAT

Basic information

species Zea mays
transcript AC234171.1_FGT001
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC234171.1_FGT001 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g24930.2 (Oryza sativa), 3'ss of exon 1
gtaggtgtcctagctagctcttgctcttgctcttgggagcaaggggagtacgtacgtatcagcaaccgatcgactgcttgctcctcacacctcgatggatcgttcgtgcgtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCGGCGCCGCCAAGGGGCTGGCTTTCCTCCACGCCGCCAACACGCCCGTCAT---
||| | | |||||| || |||| || | | | || || | || ||| || | || | | ||||| || || | | ||||||||| ||| ||||| ||||||||||||| || |||||| | |||||||||||||||||||| || || |||||||||| |||| ||| ||||||||
gtacgca-cttagctatagctagctccggccac----atctccgtttccgcgc-cgccgccgccgccg-ccgccggcacaaactgaccgattcgatccat-gtccatat---tgtgcagGGATATCGGCGACGG---TGCCGTGGGGCACGCGTCTGAAGATCGCCATCGGCGCCGCCAAGGGCCTCGCCTTCCTCCACGGCGCCTCCACCCCCGTCATCTA
















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|74232470|gb|DT640384.1|DT640384
EST:     CTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAGGAGTA                         GGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCG
genomic: CTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAGGAGTAgtaggtgtcc ... gtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCG
EST: gi|149104113|gb|EE289546.2|EE289546
EST:     CTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAGGAGTA                         GGATCTCGACGACGACGCTGCCGTGGGGCACCCGGC
genomic: CTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAGGAGTAgtaggtgtcc ... gtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGC
EST: gi|148941630|gb|EC886571.2|EC886571
EST:     CTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAGGAGTA                         GGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCG
genomic: CTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAGGAGTAgtaggtgtcc ... gtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCG

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 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 5

CTGGTCAGGCTGCTGGGCTACTGCTGCGAGGACGAGGAGCGCCTGCTCGTCTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAGGAGTAgtaggtgtcc ... gtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCGGCGCCGCCAAGGGGCTGGCTTTCCTCCACGCCGCCAACACGCCCGTCAT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 12

CTGGTCAGGCTGCTGGGCTACTGCTGCGAGGACGAGGAGCGCCTGCTCGTCTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAGGAGTAgtaggtgtcc ... gtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCGGCGCCGCCAAGGGGCTGGCTTTCCTCCACGCCGCCAACACGCCCGTCAT


Block sizes: 36 (upstream exon), 47 (downstream exon)
Score: 9

CTGGTCAGGCTGCTGGGCTACTGCTGCGAGGACGAGGAGCGCCTGCTCGTCTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAGGAGTAgtaggtgtcc ... gtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCGGCGCCGCCAAGGGGCTGGCTTTCCTCCACGCCGCCAACACGCCCGTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgatcgactgcttgctcctcacacctcgatggatcgttcgtgcgtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCGGCGCCGCCAAGGGGCTGGCTTTCCTCCACGCCGCCAACACGCCCGTCAT
                 tcctcac  putative branch site (score: 9)