Sequence
atgc intronic sequence ATGC exonic sequencegtctgtccacctacttctactgttggctagtactaccccttaattttatacaaatatgctatatattctttgaataaataatttacaagtaacttacaacatatatatagGTCCGAGATGGCATGCGTTTTGTTGAAGTTGCGCTCCTGGAACCAGAAAAGAATGTTGTGGCATTAGCTGATGCATACTTTTTCCCACCATTCCAACCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os04g04950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 2
----------gtctgtccacctacttctac-tgttggctagtactaccccttaatttta-tacaaatatgctatatatt--ctttgaataaataatttacaagtaact--tacaacatatatat-------------------agGTCCGAGATGGCATGCGTTTTGTTGAAGTTGCGCTCCTGGAACCAGAAAAGAATGTTGTGGCATTAGCTGATGCATACTTTTTCCCACCATTCCAACCAT
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gtacataactcattttcctccttggtatacattttgcttggctatactaccaagtaatggcaaaactgtgctagacattgcccatcaagctataacctctatattactgtttctgcatgttgatgaagttctttgatcatcttagGTGAGGGATGGCATGCGCTTTATTGAAGTAGACCTGGTAGAACCAGAAAAGCAAGTTGTTGCATTAGCAGATGCATATTTCTTCCCTCCTTTCCAACCAT
upper sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 2
--------------------------gtctgtccacctacttctactgttggctagtactaccccttaattttata----caaatatgctatatattctttgaataaataatt-tacaagtaacttacaacatata--tat-agGTCCGAGATGGCATGCGTTTTGTTGAAGTTGCGCTCCTGGAACCAGAAAAGAATGTTGTGGCATTAGCTGATGCATACTTTTTCCCACCATTCCAACCAT-
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tacataactcattttcctccttggtatacattttgcttgggtttactaccaagtaatggcaaaactgtgttagacattgcccatcaagctataacctctctatattactgtttatgcatgttgatgaagttctttgattatcaggTGAGGGATAGCATGCGCTTTATTGAAGTAGACCTGGTAGAACCAGAAAAGCAAGTTGTTGCATTAGCAGATGCATATTTCTTCCCTCCTTTCCAACCATC
upper sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------gtctgtcc--acctacttctac--tgttggctagta------ctaccccttaattttatacaaatatgctatatattctttgaataaataatttaca-agtaacttacaa---catatatatagGTCCGAGATGGCATGCGTTTTGTTGAAGTTGCGCTCCTGGAACCAGAAAAGAATGTTGTGGCATTAGCTGATGCATACTTTTTCCCACCATTCCAACCAT
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gttgtttactactgtaaacgcatgtttgaactgaattagttttgcattgtaatttaatgaagaatttatttgcaatgttgatatagggtttgttctcattcttgtatttgctcatggaaagagtaaaatggattctcatttttttagGTCAGAGATAGCATGCGGTTTGTTGAAGTGGTTCTGGTGGAACCAGAAAAACATGTTGTTGCACTGGCAGATGCATATTTCTTCCCTCCTTTCCAGCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctatatattctttgaataaataatttacaagtaacttacaacatatatatagGTCCGAGATGGCATGCGTTTTGTTGAAGTTGCGCTCCTGGAACCAGAAAAGAATGTTGTGGCATTAGCTGATGCATACTTTTTCCCACCATTCCAACCAT
aacttac putative branch site (score: 2)
aataaataatttacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtccacctacttctactgttggctagtactaccccttaattttatacaaatatgctatatattctttgaataaataatttacaagtaacttacaacatatatatagGTCCGAGATGGCATGCGTTTTGTTGAAGTTGCGCTCCTGGAACCAGAAAAGAATGTTGTGGCATTAGCTGATGCATACTTTTTCCCACCATTCCAACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT