Sequence
atgc intronic sequence ATGC exonic sequencegttacatttctgcaaccttaaaattgttagcattttgtcgaaatgcattggttctgctctttgctcagatatgatctgaacttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCACCCGCGCTACATGCACGGTGCTGCTACTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g47290.3 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 7
gttacatttctgcaaccttaaaattgttagcattttgtcgaaatgcattggttctgctctttgct-cagatatgatctgaacttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCACCCGCGCTACATGCACGGTGCTGCTACTAG
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-----gttagtttaacctttaaattgctggcacttagctttaccccacca-ttttgcattaccctgtttgctttttttaaattccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG
upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 7
gttacatttctgcaaccttaaaattgttagcattttgt--cgaaatgcattg----gttctgctctttgctcagatatg-------atctgaacttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCACCCGCGCTACATGCACGGTGCTGCTACTAG
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-----gttagggtaaccttaaa-ctgttggcacttagctccgcaccaccttcttgcattaccctgtttgctcatattttttctttcatttaaattatgtttagGGTGAGACCAATATAAAGCCATTGTGGGGTACTGCACAGCTCTTTATGCATCCTCGTTACATGCACGGAGCTGCTACTAG
upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 6
gttacatttctgcaaccttaaaattgttagcattttgtcgaaatgcattggttctgct--ctttgctcagatatgatctgaacttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCACCCGCGCTACATGCACGGTGCTGCTACTAG
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-----gttagtttaacctttaaattgctggcacttagctgtaccccaccattttgcattaccctgtttgcttttttttttaattccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACATGCATGGCGCTGCTACGAG
upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G544990_T01 (Zea mays), 3'ss of exon 6
gttacatttctgcaaccttaaaattgttagcattttgtcgaaatgcattggttc-tgctctttgctcagatatgatctgaacttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCACCCGCGCTACATGCACGGTGCTGCTACTAG
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-----gttagtttaacctttaaattgctggcacttagctgtaccccaccattttgcattaccctgtttgctttttttttaattccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACCGCACAGCTCTTTATGCATCCACGTTACGTGCATGGCGCTGCTACGAG
upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G335948_T01 (Zea mays), 3'ss of exon 5
gttacatttctgcaaccttaaaattgttagcattttgtcgaaatgcattggttctgctctttgctcagatatgatctgaacttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCACCCGCGCTACATGCACGGTGCTGCTACTAG
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-----gttagtttaacctttaaattgctggcacttagctgtaccccacca-ttttgcattaccctatttgctttttttaattccatttagGGTGAGACCAATATAAAGCCATTGTGGGGTACTGCACAGCTCTTTATGCATCCTCGTTACATGCACGGAGCTGCTACTAGMapped 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|29625366|gb|CB630377.1|CB630377EST: AAACAAATAAAAATTTGGATGAGATAGTTGAACTGGCAAAGAAACTCCAG GAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCAC
genomic: AAACAAATAAAAATTTGGATGAGATAGTTGAACTGGCAAAGAAACTCCAGgttacatttc ... cttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCAC
EST:
gi|29637953|gb|CB642962.1|CB642962EST: AAACAAATAAAAATTTGGATGAGATAGTTGAACTGGCAAAGAAACTCCAG GAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCAC
genomic: AAACAAATAAAAATTTGGATGAGATAGTTGAACTGGCAAAGAAACTCCAGgttacatttc ... cttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcgaaatgcattggttctgctctttgctcagatatgatctgaacttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCACCCGCGCTACATGCACGGTGCTGCTACTAG
atatgat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacatttctgcaaccttaaaattgttagcattttgtcgaaatgcattggttctgctctttgctcagatatgatctgaacttcatgcagGAGGAGACCAATATAAAACCACTGTGGGGGACTGCACAGCTTTTCATGCACCCGCGCTACATGCACGGTGCTGCTACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT