Sequence
atgc intronic sequence ATGC exonic sequencegtacagtcatgctaatatattcttttttgaaaggaaattatagtaaaccagacggaaggaaaactcttactccccaaatcctcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g01470.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G098039_T01 (Zea mays), 3'ss of exon 3
gtacagtcatgctaatatattcttttttgaaaggaaattatagtaaaccagacggaaggaaaactcttactccccaaatcctcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
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gtacagtca----agagtcaactgttccaatgttcggtgagatgaaacgaaa--gaaggaaaatatttacttacactatatccttatttcagATTCTCAACCCAAATCCAGAGGCGATGTCAAAGATTGTAACAGAGAATTCAAGTGAGGAGTTCTTGTACGCCTTGAGTAACTACTGTGCTCTTCAG
upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 3
---gtacagtcatg----ctaatatattcttttt-tgaaaggaaattatagtaaaccagacggaaggaaaactcttactccccaaatcctcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
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ttttagcagtcatgagttttaatgaatttggtttatccttgggtgttttggcatcatcatttgattaatacaaatttttctattggttggctccctgcagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAACGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTTCACTTCAG
upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 3
----gtacagtcatg----ctaatatattcttttttgaaaggaaattatagtaaaccagacggaaggaaaactcttactccccaaatcctcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
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cttttagcagtcatgagtcttaatgaattggtttatccttgggtgttttgacatcatcgtttgattaatacaaatttttctattgattggttccctgtagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAATGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTGCACTTCAG
upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 4
-----gtacagtcatgctaatatattcttttttgaaaggaaattatagtaaaccagacggaaggaaaactc-ttactccccaaatcc--tcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
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ttctgataaaatattgaactaccactcaccatcagctcttatgtttttggtatcagctttttgacttatttgttgtttcccctgtttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAGMapped 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|29630290|gb|CB635299.1|CB635299EST: GCAGAGACAATAAAATTGAACTTGATCGCATTGTTGGATGCATACCACAG ATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCC
genomic: GCAGAGACAATAAAATTGAACTTGATCGCATTGTTGGATGCATACCACAGgtacagtcat ... cccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatagtaaaccagacggaaggaaaactcttactccccaaatcctcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
ctcttac putative branch site (score: 3)
ctcttactccccaaat CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagtcatgctaatatattcttttttgaaaggaaattatagtaaaccagacggaaggaaaactcttactccccaaatcctcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG