Sequence
atgc intronic sequence ATGC exonic sequencegtttggttgtttgagtcctacacaattatacacttcattaaacttttatcaaaagatttactggttttatgtgtttattcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G124091_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 6
gtttggttgtttgag-tcctacacaattata-cacttcattaaacttttatcaaaagattt-actggttttatgtgtttattcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
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gtttggacttctaatctcctacaaacttaaagcatctcattaatttgcctttataagctaagaataatcttgtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG
upper sequence: GRMZM2G124091_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT3G48540.1 (Arabidopsis thaliana), 3'ss of exon 6
---gtttggttgtttgagtcctacacaattatacacttcattaaacttttat-caaaagatttac------tggttttatgtgttt--attcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
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tatagaaaacttagggaactctgctgcagtttctgttccgaagtatttgtgtgtggatggtttatatgagtttgttttgtgctcctcgaatctcttgcagAAGCTTTATGTGACAATGTTCCCTTGCAATGAATGTGCCAAGATTATTTTACAG
upper sequence: GRMZM2G124091_T04 (Zea mays), 3'ss of exon 6
lower sequence: PP1S426_43V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------------------------gtttggttgtttgagtcctacacaattatacacttcattaaacttt-tatcaaaagatttactggtt---ttatgtgtttattctttta-------cagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
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gtaagcttccaggttgtgtcatgcttggcctgattagaaccagtttttcgaacttaaggtgaaaaagctttagtagttga-tccagaagctttttacttttctaaaaatagtatactagtcgttgtttctgtcaagtaagatgcataccttgtgaaatgtggcagAGACTGTACGTGACCCTCTTCCCTTGCAATGAATGTGCCAAGATAATTATTCAGMapped 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|211283832|gb|FL366650.1|FL366650EST: CTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAG AAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATT
genomic: CTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAGgtttggttgt ... tcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATT
EST:
gi|89253024|gb|DY624810.1|DY624810EST: CTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAG AAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATT
genomic: CTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAGgtttggttgt ... tcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATT
EST:
gi|101399938|gb|EB821816.1|EB821816EST: CTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAG AAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATT
genomic: CTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAGgtttggttgt ... tcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATT
EST:
gi|149000975|gb|EE038215.2|EE038215EST: CTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAG AAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATT
genomic: CTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAGgtttggttgt ... tcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATT
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:
47 (upstream exon),
49 (downstream exon)
Score:
40CTACGTTGTCCATGCTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAGgtttggttgt ... tcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
Block sizes:
46 (upstream exon),
47 (downstream exon)
Score:
9CTACGTTGTCCATGCTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAGgtttggttgt ... tcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
Block sizes:
39 (upstream exon),
47 (downstream exon)
Score:
6CTACGTTGTCCATGCTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAGgtttggttgt ... tcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
Block sizes:
44 (upstream exon),
14 (downstream exon)
Score:
5CTACGTTGTCCATGCTGAGGTTAATGCAATTCTAAATACCAACCATGCTTCAGCGGCTGGACAGgtttggttgt ... tcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcattaaacttttatcaaaagatttactggttttatgtgtttattcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
tttattctttt CT-rich tract
taaacttttatcaaaa TA-rich tract