Sequence
atgc intronic sequence ATGC exonic sequencegttagcagtttccctacattttttgtgcgcgtgttggaaatcaccaagcgaaatggttgtaaagtttggcctggttgatgcagGTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g01430.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g01430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 6
gttagcagtttc-cctacattttttgtgcgcgtgttggaaatcaccaagcgaaatggttgtaaagtttggcc-----tggttgatgcagGTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG
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gtttgctgtctcgtctgcattacatatatgc----ttaaaattctggcaagaagtcattaaaaagtcagtctaccatttgttggtgcagGTGTCGTAGAGTTAGTTGCAGACCATGTAGTTTGTGAGGAAGGAAAGCCCCTTTCGCCAGAAGCAGCACAGATTCTG
upper sequence: LOC_Os12g01430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G477632_T01 (Zea mays), 3'ss of exon 5
gttagcagtttc-cctacattttttgtgcgcgtgttggaaatcaccaagcgaaatggttgtaaagtttggcc-----tggttgatgcagGTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG
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gtttgctgtctcgtctgcattacatatatgc---ttaaaattctgccaa-gaggtcattaaaaagtcagtctaccatttgttggtgcagGTGTCGTAGAGTTAGTTGCAGACCATGTAGTTTGTGAGGAAGGGAAGCCCCTTGCGCCAGAAGCAGCATAGACTCTG
upper sequence: LOC_Os12g01430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G467086_T01 (Zea mays), 3'ss of exon 6
gttagcagtttc-cctacattttttgtgcgcgtgttggaaatcaccaagcgaaatggttgtaaagtttggcctggttgatgcagGTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG
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gtttgcagtctcgtctgcattacatatgtgc---ttagaatctgccaagtt--gtcgttaaaaagtctaccattgttgttgcagGTGTTGTAGAGTTGGTTGCAGACCATGTAGTTTGTGAGGAAGGAAAGCCCCTTTCGCCAGAAGCAGCGCAGACTCTGMapped 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|218485998|gb|FG965622.1|FG965622EST: AATGGAACCCTTTCTACGCAAGCAAGGAATGCCAGTTCGTCTGAACAAAG GTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCA
genomic: AATGGAACCCTTTCTACGCAAGCAAGGAATGCCAGTTCGTCTGAACAAAGgttagcagtt ... gttgatgcagGTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCA
EST:
gi|33686640|gb|CF314879.1|CF314879EST: AATGGAACCCTTTCTACGCAAGCAAGGAATGCCAGTTCGTCTGAACAAAG GTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCA
genomic: AATGGAACCCTTTCTACGCAAGCAAGGAATGCCAGTTCGTCTGAACAAAGgttagcagtt ... gttgatgcagGTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgtgttggaaatcaccaagcgaaatggttgtaaagtttggcctggttgatgcagGTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG
ggttgat putative branch site (score: 5)
taaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcagtttccctacattttttgtgcgcgtgttggaaatcaccaagcgaaatggttgtaaagtttggcctggttgatgcagGTGCGGTAGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC