Sequence
atgc intronic sequence ATGC exonic sequence...tgcataaattgtgtttgtcttttgttaccacacaattacaaatgctacttcatgtatatgctgctttatgatatgacattgctcaaatatcttattacagGTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17180.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 2
-------tgcataaattgtgtttgtcttttgttaccacacaattacaaatgctacttcatgtatatgctgctttatgatatgacattgctcaaatatcttattacagGTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATG
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ctattctttgatatgtgatattgtgattagactgaaacatacata-aattgcgaggttaaaggaatacaaaatggtga-atgctattact-----atctttctgcagGTTTGGTCGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTGGTCAGTATGGAGCCTGAAAAGGCTGAATG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 2
tgcataaattgtgtttgtcttttgttaccacac--aattacaaatgctacttcatgtatatgctgctttatgatatgacattgctcaaatatcttattacagGTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATG
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-cagtagctattctttgatctgtgtgactagactgaagtatgcataaattgtgaggt-taaaggaatacaaaatagtaaatgctattactatctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 2
tgcataaattgtgtttgtcttttgttaccacacaa--ttacaaatgctacttcatgtatatgctgctttatgatatgacattg---ctcaaatatcttattacagGTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATG
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-----aatttgtaaattccagttattgccttgtggacttatggatttttgttttgcaaatttcaaatgaatggttttcctctggagctcatttcctttgtcacagGTTTGGTTGAGACTGATCCAGAAGGTGCACTTGCTGGCTTTGCTGAAGTAGTTCGCATGGAACCAGAGAAGGCAGAGTGMapped 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|6431605|gb|AU081257.1|AU081257EST: ACCAGTACTACAACTCCAAAG GTCTGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAG
genomic: ACCAGTACTACAACTCCAAAGgttcgcttcc ... cttattacagGTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAG
EST:
gi|6431604|gb|AU081256.1|AU081256EST: GATGTTGACATCGAGAACCAGTACTACAACTCCAAAG GTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAG
genomic: GATGTTGACATCGAGAACCAGTACTACAACTCCAAAGgttcgcttcc ... cttattacagGTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacttcatgtatatgctgctttatgatatgacattgctcaaatatcttattacagGTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATG
tcttatt CT-rich tract
tcaaatatcttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcataaattgtgtttgtcttttgttaccacacaattacaaatgctacttcatgtatatgctgctttatgatatgacattgctcaaatatcttattacagGTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATG
tgcataa
- - - - - -tgtttgt
- - - - - - - - - cttttgt
- - - - - - - - - - - - - - cacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctcaa