Sequence
atgc intronic sequence ATGC exonic sequence...ttatgagttttttgtttgatgccctacatctacttcagttttggtaaaagttccaatgtatctaatggttgatatgttgtcttgttatttcataacacagGTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62040.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62040.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 2
ttatgagttttttgt-ttgatgccct---acatctacttcagttttggtaaaagttccaatgtatctaatggttgatatgttgtcttgttatttcataacacagGTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTA
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--aaatgttactgatgttgataagctgtgatgcttgctggattcactgtagcatttatgctataatcttctgatgtttccttcccctgtcactgc--aatgcagGTCCCATTCTGTCCTATGGTAGGATCAGAAGTGTACTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTAGAGCTATAGGTTTGCGTA
upper sequence: LOC_Os01g62040.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G018697_T02 (Zea mays), 3'ss of exon 2
---ttatgagttttttgtttgatgccctacatctacttcagttttggtaaaagttccaatgta-tctaatggttgatatgttgtcttgttatttcataacacagGTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTA
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ggtgttctaggggacagtccgataaaatgcgcttgctgaagtcactgtagcacttatgttatagtctaatgttt----ccttcctctatcactatacaatgcagGTCCCTTTCTGTCCTATGGTAGGATCAGAAGTGTACTCCTCGGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTAGAGCTATAGGTTTGCGTA
upper sequence: LOC_Os01g62040.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------------------ttatgagttttttgtttgatgccctaca-tctacttcagttttggtaaaagttccaatgtatctaatggttgatatgttgtcttgttatttcataacacagGTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTA
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gtacaacttaaatgtactcttaccattttttgttcagtagtgtcttgaattctctttatcagagctgtagatttagattctggggttctctccagttgattttcagtctagctctgggatgttgaatgccttactct-tcaggggtgtgagat-ctgctttttacttctgatttacagGTTCCTTTCTGCCCAATGGTGGGATCAGAGGTATACTCATCAGAGGTAAAGAAAACTGAGATTTTAATGGAAAATTTCCGACGGGCTATTGGTCTACGTAMapped 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|33676655|gb|CF304894.1|CF304894EST: CCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAG GTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAG
genomic: CCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgttggtgctt ... cataacacagGTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagttccaatgtatctaatggttgatatgttgtcttgttatttcataacacagGTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTA
tcataac putative branch site (score: 2)
ttatttc CT-rich tract
ttgttatttcataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgagttttttgtttgatgccctacatctacttcagttttggtaaaagttccaatgtatctaatggttgatatgttgtcttgttatttcataacacagGTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - tgatgcc
- - - - - - - - - - - -ctacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggttg