Sequence
atgc intronic sequence ATGC exonic sequencegtgattgtcgatgtctccattttcttctgatggttcactacttctgaatacaaagttctgaatttcatataccgagaaactcatcagaatgttaattctgcagGTGTGCTTTACTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04660.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G174343_T07 (Zea mays), 3'ss of exon 1
gtgattgtcgatgtctccattttcttctgatggttcactacttctgaatacaaagtt-ctgaatttcatat-accgagaaactcatcagaatgttaattctgcagGTGTGCTTTACTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGA
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gttatttgtaatccccctgctatcttctgtcagtttacttcttcagtgtgctgagttgctgactgacatgtcgctgaataattcgttcgtgtataaattctccagGTGTTCTTTTCGCTGTGCTGATAACTGCAGTTTTTACCGATGTGATAAAGACTGCAGTAGGGAGACCGAGGCCAGACTTCTTCTGGCGATGCTTTCCTGA
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0006g02480.t01 (Vitis vinifera), 3'ss of exon 2
-----gtgattgtcgatgtctcc--attttcttctgatggttcactacttctg-aatacaaagttctgaatttcatataccgagaaactcatcagaatgttaattct-----gcagGTGTGCTTTACTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGA
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gtgataagatctttggctcctcatggtttatctgtaataattcctcttgtatgcaataggaattgatgtgttatttgaaagattgaactgatggtttgatttatttgctagagcagGCCTGTTATTCTCTGTTCTGGTAACAGTGGTTATTACTGATGCAATAAAAAATGCAGTTGGTCGACCTCGACCAGACTTCTTTTGGCGTTGTTTTCCTGA
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0011g04170.t01 (Vitis vinifera), 3'ss of exon 4
gtgattgtcgatgtctccattttcttctgatggttcactacttctgaatacaaagttctgaatttcatataccgagaaactcatcag--aatgttaattct-----gcagGTGTGCTTTACTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGA
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gt-actatt-atatatataaaaccccaaaggggataattttttttgctcctatttaaaggaagtgcctatgaaggtaaatctgctgactgatatgaattcacgaaagcagGCCTCTTTTTTTCTATGCTGATCACTGCGGTTATTACGGAAGCAATAAAAGATGCAGTTGGACGGCCTCGGCCAGACTTCTTTTGGCGCTGCTTTCCTGA
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0011g04160.t01 (Vitis vinifera), 3'ss of exon 4
gtgattgtcgatgtctccattttcttctgatggttcactacttctgaatacaaagttctgaatttcatataccgagaaactcatcag-aatgttaattct-----gcagGTGTGCTTTACTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGA
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----gtactattatatatataaaaccccaaggggataattttttttgctcctatttaaaggaagt-gcctatgaaggtactgctgactgatatgaattcacgaaagcagGCCTCTTATTTTCTGTGCTGATCACTGCGGTTATCACGGATGCAATAAAAGATGCAGTTGGACGGCCTCGGCCAGACTTCTTTTGGCGCTGCTTTCCTGAMapped 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|218497722|gb|FG949370.1|FG949370EST: CGTTTATATCGCTAGGAGAGATGTCTATGATCTTCATCACGCAACATTAG GTGTGCTTTACTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGA
genomic: CGTTTATATCGCTAGGAGAGATGTCTATGATCTTCATCACGCAACATTAGgtgattgtcg ... aattctgcagGTGTGCTTTACTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaaagttctgaatttcatataccgagaaactcatcagaatgttaattctgcagGTGTGCTTTACTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGA
tgttaat putative branch site (score: 3)
aatttcatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattgtcgatgtctccattttcttctgatggttcactacttctgaatacaaagttctgaatttcatataccgagaaactcatcagaatgttaattctgcagGTGTGCTTTACTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA