Sequence
atgc intronic sequence ATGC exonic sequencegtggttttggaagcaattgaaaattcatgtgttgttcttttgtgcttgaaatgcaaatctgacataaattgttgttgtgtatgtgttttcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g07080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g07080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G303752_T01 (Zea mays), 3'ss of exon 2
gtggttttggaagcaattgaaaattcatgtgttgttcttttgtgcttga---aatgcaaatct---gacataaattgttg----------ttgtgtatgtgttttcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC
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gtggtttcagagacaac-ggaaccctttatgtgatccttttatgctgaatttggtgaaaatgttgtggcatttatgttagctccatttgtttttgtgtatgcatgggaagcagATTTTGATCCTAGATGAGGCTGATAGGCTCTTGGATATGGGATTCCAGAAACATATTAACTTCATACTTTCAATGTTGCCAAAGCTGAGGAGGACTGGGC
upper sequence: LOC_Os01g07080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G367714_T01 (Zea mays), 3'ss of exon 4
gtggttttggaagcaattgaaaattcatgtgttgttcttttgtgcttga---aatgcaaat---------------ctgacataaattgttgttgtgtatgtgttttcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC
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gtggtttcagagacaacggaaccctc-tgtgtgatccttttctgctgaatttagtgaaaatgttgtggcatttatgttagctccatttgtttttgtgtatgtgtgg--gaagcagATTTTGATCCTAGATGAGGCTGATAGGCTCTTGGATATGGGATTCCAGAAACATATTAACTTCGTACTTTCAATGTTGCCAAAGCTGAGGAGGACTGGGC
upper sequence: LOC_Os01g07080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G125947_T01 (Zea mays), 3'ss of exon 2
gtggttttggaagcaattgaaaattcatgtgttgttcttttgtgcttga---aatgcaaat---------------ctgacataaattgttgttgtgtatgtgttttcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC
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gtggtttcagagacaacggaaccctc-tgtgtgatccttttctgcttaatttggtgaaaatgttgtggcatttatgttagctccatttgtttttgtgtatgtgtgg--gaagcagATTTTGATCCTAGATGAGGCTGATAGGCTCTTGGATATGGGATTCCAGAAACATATTAACTTCATACTTTCAATGTTGCCAAAGCTGAGGAGGACTGGGC
upper sequence: LOC_Os01g07080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G02760.1 (Glycine max), 3'ss of exon 2
gtggtt-ttggaagca-attgaaaattcatgtgttgttcttttgtgcttgaaatgcaaatctgacataaattgttgttgtgtatgtgttt-tcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC
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gaagttgttggaaaaatattccgaatagagtatttgatttgactttttttttatttttttttattttagccagttgacattattatgactgttcttacagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATAACTCTCTTGCCTAAGCTTCGGAGAACTGGTC
upper sequence: LOC_Os01g07080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 2
gtggttttggaagcaattgaaaattcatgtgttgttcttttgtgcttgaa-atgcaaatctgacat----aaattgttgttgtgtatgtgttttcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC
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attatttgatttggtgtattacacccccccctcccccccccccccccacacacacacacactattttagcaatttgacattat-tatgattattctta-cagATTTTGATTTTGGATGAGGCTGATAGACTCTTAGATATGGGATTCCAGAAGCAGATAACTTCTATTATATCTCTCTTGCCTAAGCTTCGGAGAACTGGTC
upper sequence: LOC_Os01g07080.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0067g01900.t01 (Vitis vinifera), 3'ss of exon 2
---gtggttttggaagcaattgaaaattcatgtgttgttcttttgtgcttgaaatgcaaatctgacataaattgttgttgtgtatgtgttt-tcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC
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gaaatttcctcttgctgagtatgatatccttttggatttttaccaagtttgtttcaaaataattaaatttat-actcctgaatttttgttggttggaacagATTTTGATTTTGGACGAGGCTGATAGGCTTTTAGATATGGGATTCCAGAAGCAAATTACTTCCATCATTGCTCGCCTACCAAAGCTTCGCAGAACTGGTCMapped 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|29639070|gb|CB644079.1|CB644079EST: TGTTCGACGTAATGGAGCGCTTAGACACTCTGAACTACAAGAATCTTGAG ATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAG
genomic: TGTTCGACGTAATGGAGCGCTTAGACACTCTGAACTACAAGAATCTTGAGgtggttttgg ... ttcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttgaaatgcaaatctgacataaattgttgttgtgtatgtgttttcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC
atctgac putative branch site (score: 3)
tgttttc putative PPT
ataaattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggttttggaagcaattgaaaattcatgtgttgttcttttgtgcttgaaatgcaaatctgacataaattgttgttgtgtatgtgttttcgaagcagATTTTGATCCTGGATGAAGCTGATAGGCTGTTGGATTTAGGATTCCAGAAGCAGATTACGTCGATTATTTCGAAGTTGCCAAAGCTGAGGAGAACAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA