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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCCCTCCCACCTCGCCGCGGCAGCCATGGCGATCACGGCGCCAACTCCCGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccgccacccctttcattccaccagattcctccgtggcgtgcggggtttgtgagatctagtggctcgagtagccatctggcagcgcactggcttaattaatcttttttttcttgtttgatcgcag

Basic information

species Zea mays
transcript GRMZM2G110626_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110626_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 1
CTCCCCTCCCACCTCGCCGCGGCAGCCATGGCGATCACGGCGCCAACTCCCGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaa-------------cagccgccacccctttcattccaccagattcctccgtggcgtgcggggtt--tgtgagatctagtggctcgagtagccatctggcagcgcactggcttaattaatcttttttttcttgtttgatcgcag
||| || ||  |  || ||  |  |||||||||||||| || |  || |||||||||| ||||||||| |||||||||||||||||||||||||| ||||||||             |  | || | ||||| |   || |||||||||   | | || |  |||||  ||| |||||||||||| ||| | ||| || ||   |||   |  || |||          | ||| | |||| ||||
CTCGCCGCCGCCGCCGTCGTCGTCGCCATGGCGATCACCGCCCAGACCCCCGACATCCTCGGCGAGCGCCAGTCCGGCCAGGACGTCCGCACGCAAAACGgtaactcgtctctccccctcctgcaagcccttccccgccgccagattccgtggagtcgcggcgggtttttgtaagatctagtggcacgactcgccgtccgg--acgcggggatttgatt----------tccttctctgattgcag
















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|211160355|gb|FL101555.1|FL101555
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211160352|gb|FL101552.1|FL101552
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211160359|gb|FL101559.1|FL101559
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211160360|gb|FL101560.1|FL101560
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211158769|gb|FL101548.1|FL101548
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211158771|gb|FL101550.1|FL101550
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|22491073|gb|BU050996.1|BU050996
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211160354|gb|FL101554.1|FL101554
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211160357|gb|FL101557.1|FL101557
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211160358|gb|FL101558.1|FL101558
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211160351|gb|FL101551.1|FL101551
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
EST: gi|211160353|gb|FL101553.1|FL101553
EST:     CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACG                         TGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG
genomic: CGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCG

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), 48 (downstream exon)
Score: 75

CTCCCCTCCCACCTCGCCGCGGCAGCCATGGCGATCACGGCGCCAACTCCCGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 27

CTCCCCTCCCACCTCGCCGCGGCAGCCATGGCGATCACGGCGCCAACTCCCGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 32

CTCCCCTCCCACCTCGCCGCGGCAGCCATGGCGATCACGGCGCCAACTCCCGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 48

CTCCCCTCCCACCTCGCCGCGGCAGCCATGGCGATCACGGCGCCAACTCCCGACATCCGCGGCGAGCGTCAGTCCGGCCAGGACGTCCGCACGCAGAACGgtaacagccg ... ttgatcgcagTGATGGCGTGCGGCGCGTTGTCCAACATCGTAAAATCCTCGCTCGGCCCCGTCGGTCTCGACAAG