Sequence
atgc intronic sequence ATGC exonic sequence...acgaattatgtacttactaacatgcatggtgaattattaatctgtttaattctcgatctgttcttgtgtttttctgaacgaattactgttctcgctgcagGACTGTTTCGGGCGACCGATAGCCAGCAAGCCTGATGCGTGGTTCGATGTGGTTGAGCGCTACTCGACTGACAGCAACAAGACACTGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g70360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g70360.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 2
acgaattatgtacttactaacatgcatggtgaattattaatctgtttaattctcgatctgtt-cttgtg----tttttctgaacgaattactgttc---tcgctgcagGACTGTTTCGGGCGACCGATAGCCAGCAAGCCTGATGCGTGGTTCGATGTGGTTGAGCGCTACTCGACTGACAGCAACAAGACACTGCA
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--------tgtgactactagatcgcatcataatgtaattagcaatgcaggtatgtgattgtgacttatgaagttttttataattttttttttgtttgttttttcgcagGACTGTTTTGGGAGACCAATTGCAAGTGCTCCTGATGCTTGGTTTGATGTTGTCGAACGCTACTCGAATGATAACAACAAGACACTGAA
upper sequence: LOC_Os01g70360.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------acgaattatgtacttactaac-atgcatggtg-aattatta-atctgtttaattctcgatctgttcttgtgtttttctgaacga---------attactgttctcgctgcagGACTGTTTCGGGCGACCGATAGCCAGCAAGCCTGATGCGTGGTTCGATGTGGTTGAGCGCTACTCGACTGACAGCAACAAGACACTGCA
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gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcattgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAAMapped 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|33678345|gb|CF306584.1|CF306584EST: GCGTTGGGAAGGAGGATTTCTACATCCGCCGCTTCTTCCGCCGCGTCCAG GACTGTTTCGGGCGACCGATAGCCAGCAAGCCTGATGCGTGGTTCGATGTG
genomic: GCGTTGGGAAGGAGGATTTCTACATCCGCCGCTTCTTCCGCCGCGTCCAGgtgagctcac ... ctcgctgcagGACTGTTTCGGGCGACCGATAGCCAGCAAGCCTGATGCGTGGTTCGATGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaattctcgatctgttcttgtgtttttctgaacgaattactgttctcgctgcagGACTGTTTCGGGCGACCGATAGCCAGCAAGCCTGATGCGTGGTTCGATGTGGTTGAGCGCTACTCGACTGACAGCAACAAGACACTGCA
gtttaat putative branch site (score: 4)
ctgttctc putative PPT
tgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acgaattatgtacttactaacatgcatggtgaattattaatctgtttaattctcgatctgttcttgtgtttttctgaacgaattactgttctcgctgcagGACTGTTTCGGGCGACCGATAGCCAGCAAGCCTGATGCGTGGTTCGATGTGGTTGAGCGCTACTCGACTGACAGCAACAAGACACTGCA
- - - - - - - -actaaca
- - - - - - - - - - - tgcatgg
- - - - - - - - - - - - - - - - - - - - tctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgtt