Sequence
atgc intronic sequence ATGC exonic sequence...taaagttagtagttggctatactattaaacttgctcttagctatagttaattatgatgttgtggctgacggagagatttatattatgttgggcgatgcagGATTACACGGCGAAGCTCTCGGACTTCGGGCTGGCCAAGGAGGGCCCGCAGGGGGACGCGACACACGTCACGACCCGCGTCATGGGGACCCACGGGTACG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g53750.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g53750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G166027_T01 (Zea mays), 3'ss of exon 3
taaagttag-tagttggc-tatactattaaacttgctcttagcta-tagttaattatgatgttgtggctgacggagagatttatattatgttgggcgatgcagGATTACACGGCGAAGCTCTCGGACTTCGGGCTGGCCAAGGAGGGCCCGCAGGGGGACGCGACACACGTCACGACCCGCGTCATGGGGACCCACGGGTACG
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tacccttatctagctagcctaggatatataac--ggtcgaagcaaatatttaaacgatatgtgtagactgaatgacgtgttccttttctgt-gcatgacacagGATTACACGGCAAAGCTCTCAGACTTTGGCCTGGCCAAGGAAGGCCCACAGGGCGACGACACCCACGTCACCACCCGTGTCATGGGGACACACGGCTACG
upper sequence: LOC_Os02g53750.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G05940.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------------------------------taaagttagtagttggctatactattaaacttgctcttagctatagttaattatgatgttgtggctgacggagagatt--tatattatgttgggcgatgcagGATTACACGGCGAAGCTCTCGGACTTCGGGCTGGCCAAGGAGGGCCCGCAGGGGGACGCGACACACGTCACGACCCGCGTCATGGGGACCCACGGGTACG
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gtaagtaacaaaaaatccaacccgatttttactcttaaagtctctacagtcaaagtttttacagtcaaatttcttacagcaaaagcgtttacaaccgaaattaacagtcgttaccaatcagccctta--ttttccaatttataattcctaaagttctaaagaagctcctataccaaatcttgtttt-cagGATTACACGGCGAAACTCTCTGACTTCGGGTTAGCCAAAGACGGACCAGAAGGAGACGACACTCATGTGTCAACTCGAGTGATGGGCACACAAGGCTACGMapped 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|29682833|gb|CB679108.1|CB679108EST: CTCCGGTGATCTACCGAGACTTCAAGGCATCCAACATCCTGCTCGACTCG GATTACACGGCGAAGCTCTCGGAC
genomic: CTCCGGTGATCTACCGAGACTTCAAGGCATCCAACATCCTGCTCGACTCGgtgagtactc ... ggcgatgcagGATTACACGGCGAAGCTCTCGGAC
EST:
gi|29673917|gb|CB670192.1|CB670192EST: CTCCGGTGATCTACCGAGACTTCAAGGCATCCAACATCCTGCTCGACTCG GATTACACGGCGAAGCTCTCGGACTTCGGGCTGGCCAAGGAGGGCCCGCAG
genomic: CTCCGGTGATCTACCGAGACTTCAAGGCATCCAACATCCTGCTCGACTCGgtgagtactc ... ggcgatgcagGATTACACGGCGAAGCTCTCGGACTTCGGGCTGGCCAAGGAGGGCCCGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaattatgatgttgtggctgacggagagatttatattatgttgggcgatgcagGATTACACGGCGAAGCTCTCGGACTTCGGGCTGGCCAAGGAGGGCCCGCAGGGGGACGCGACACACGTCACGACCCGCGTCATGGGGACCCACGGGTACG
ggctgac putative branch site (score: 3)
agatttatattatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaagttagtagttggctatactattaaacttgctcttagctatagttaattatgatgttgtggctgacggagagatttatattatgttgggcgatgcagGATTACACGGCGAAGCTCTCGGACTTCGGGCTGGCCAAGGAGGGCCCGCAGGGGGACGCGACACACGTCACGACCCGCGTCATGGGGACCCACGGGTACG
- - - - - - - - - - - - - - -cttgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgttg