Sequence
atgc intronic sequence ATGC exonic sequence...taaaatcgtagtcccaaatgtatattaggaattacgacatgcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAGTAAAACTCAAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g59930.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g59930.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 7
-----taaaatcgtagtccc---aaatgtatattaggaattacgacat-gcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAGTAAAACTCAAAT
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tcatttgaagttattatcctgagaaatctgctttacgttatactaattagcacattgtttc-caaagacatccgacataca---cagtgtt-----tttacttgtgcagCCTCCTGAGAACTGGAACGGTGGTGTTGGGTTTGTGTCTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG-------------
upper sequence: LOC_Os01g59930.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 7
--taaaatcg---tagtcccaaatgtatattaggaattacgacatgcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAGTAAAACTCAAAT
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attcacatcaggctagctctccttttacaat--gttgtatgtgatgattgtttttttttatttttattttatgta-attgctgcttggactact--ctcccacagCCTCCTGAAGCATGGAACGGTGGCGTCGGGTTTGTATCCAAGGAAATGATCAAGGCCCATTGCCCTGCACCTGCATCTGACATTAAG-------------Mapped 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|117244284|gb|CT843075.1|CT843075EST: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAG CCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
genomic: TGGCCAAAACCTACCCTGATCGCTTTAAGATCTACTATGTCTTGAATCAGgtgaacccta ... gcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAGTAAAACTCAAAT
tgttgat putative branch site (score: 4)
ttttttgctt CT-rich tract
aatgttgatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaaatcgtagtcccaaatgtatattaggaattacgacatgcatggtacttgataaagacatttgcagcagattccaatgttgattttttgcttgtgcagCCTCCTGAAGTCTGGAACGGTGGCGTTGGGTTTGTGTCACAGGACATGATTAAAGCTCATTTGCCAGCACCTGCCGAGGACATTCAAGTAAAACTCAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA