Sequence
atgc intronic sequence ATGC exonic sequencegtaattaactcaaacaaatccatatacacattactactagattatcatactagtaatttaactacttctcttaattaattatagcttggatgatttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g44090.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G150841_T01 (Zea mays), 3'ss of exon 2
gtaattaactcaaacaaatccatatacacattactactagattatcatactagtaatttaactacttctcttaattaattata-gcttggatgatttctagctaattaatcaatcaaacaggaaatt--aatcagcttgaat-------tgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
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gtaggtggtgccacagtggcaggccatgcat--acagcagatccccggcccgg----ccagtttcttttatttattagctgtgtgcgatgatgatgatgaatgatccatccaatcggggatgtaattctgttcgttttgcacgtacgaatgacacagGTGGTCTCAGATTGCTTCGCAGCTGCCGGGGCGGACGGACAACGAGGTGAAGAACTTCTGGAACTCGTACGTCAAGAAGAAGCTCCGGCAGCGCGGGATC
upper sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaattaactcaaacaaatccatatacacattactactagattatcatactagtaatttaactacttctcttaattaatt-atagcttggatgatttctagctaattaatcaatcaaacag-gaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC-
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-----------------------------------------------gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttattt--ttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGC-AGCATGGGAATC
upper sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaattaactcaaacaaatccatatacacattactactagattatcatactagtaatttaactacttctcttaattaattatagcttggatgatttctagctaattaatcaatcaaaca-ggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
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-----------------------------------------ctgagacacgataaggtcacatgttggt---aataagctatcccccccccccccccccccctgctagttgggctaatgcagcaattgatccccttgcatg----cagGTGGTCTCAGATTGCAACTCAGTTACCAGGCCGCACCGACAACGAAATCAAAAACTTCTGGAACTCCTGTATCAAGAAGAAGCTTCGCAACATCGGCATC
upper sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaattaactcaaacaaatccatatacacattactactagattatcatactagtaatttaactacttctcttaattaattatagcttggatgatttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
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-----------------------------------------tcatcg-atgagaggcagaagggccggattgtagtctctgcagct-acatgtgctccttgcaaatgttgagttaaagcagaatttgatc---ctgtat-aatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATCMapped 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|58669119|gb|CK057805.1|CK057805EST: CAGGAAGAAGAAGACCTCATCATCCATCTCCATTCCATGCTAGGAAACAA GTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAA
genomic: CAGGAAGAAGAAGACCTCATCATCCATCTCCATTCCATGCTAGGAAACAAgtaattaact ... attgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
aattaat putative branch site (score: 3)
taattaatcaatcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattaactcaaacaaatccatatacacattactactagattatcatactagtaatttaactacttctcttaattaattatagcttggatgatttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC