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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACATGTACCACTGCATCTCCATGGAGGAGATCACCAGGGCCTCCGGCGCCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgtacacccgtactcgtggctgctccaccgccctgcttgtttttgccctcgcacgccgcgttaaccacaccacttgggcggttacttattactactacccatgcgtagcgtaatgctgtttatgtgttctccgttgcag

Basic information

species Zea mays
transcript GRMZM2G052630_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 5'ss of exon 3
CTACATGTACCACTGCATCTCCATGGAGGAGATCACCAGGGCCTCCGGCGCCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgtacacccgtactcgtggctgctccaccgccctgcttgtttttgccctcgcacgccgcgttaaccacaccacttgggcggttacttattactactacccatgcgtagcgtaa-tgctgtttatgtgttctccgttgcag
||||||||||||||||||  ||||||||||||||| |||||| |||||| | |||||||| || |||||||| ||||||||||||||||| |||||||| ||     || |   | |||| ||   ||   ||  ||| ||  ||     ||| |  ||       ||   || | || |        | || | |||   ||   |   ||   ||   || ||||| | | |            
CTACATGTACCACTGCATTGCCATGGAGGAGATCAGCAGGGCGTCCGGCTCGGTCGGCCTGTCTTACGGCGCTCACTCCAACCTCTGCATTAACCAGCTGgta--ctgttctgtc-tact-gtcattgtaacat-gccatgaatga----gccattaca------attggacaaaacaatct-----ctgctcaatacagttatgaacttgtgatgtgtctgatgtttgtttatag----------
















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|67030645|gb|CO459394.1|CO459394
EST:     CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTT                         GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTG--C---
genomic: CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
EST: gi|31354622|gb|CD438979.1|CD438979
EST:     CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTT                         GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
genomic: CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
EST: gi|76936508|gb|DV174756.1|DV174756
EST:     CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTT                         GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
genomic: CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
EST: gi|149079538|gb|EE168523.2|EE168523
EST:     CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTT                         GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
genomic: CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
EST: gi|91057188|gb|EB167606.1|EB167606
EST:     CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTT                         GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
genomic: CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
EST: gi|149073457|gb|EE161762.2|EE161762
EST:     CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTT                         GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG
genomic: CCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG

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: 44 (upstream exon), 36 (downstream exon)
Score: 11

CTACATGTACCACTGCATCTCCATGGAGGAGATCACCAGGGCCTCCGGCGCCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 19

CTACATGTACCACTGCATCTCCATGGAGGAGATCACCAGGGCCTCCGGCGCCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 15

CTACATGTACCACTGCATCTCCATGGAGGAGATCACCAGGGCCTCCGGCGCCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG


Block sizes: 30 (upstream exon), 45 (downstream exon)
Score: 7

CTACATGTACCACTGCATCTCCATGGAGGAGATCACCAGGGCCTCCGGCGCCGTCGGCCTCTCCTACGGCGCGCACTCCAACCTCTGCATCAACCAGCTTgtgagtcgta ... tccgttgcagGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG