Sequence
atgc intronic sequence ATGC exonic sequencegtttgggcttcaactgtattctattgcaagaatcatctgtatcattttttttgtgaggacatccaatcttggtatttctgcttggtcacatcattgataatcactaattgtgctccttttccaatccatttgttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCATATTTCAATGACCGTTCAGCTATA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g43090.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g43090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 4
gtttgggcttcaactgtattctattgcaagaatcatctgtatcattttttttgtgaggacatccaatcttggtatttctgcttggtcacatcattgataatcactaattgtgctccttttccaatccatttgttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCATATTTCAATGACCGTTCAGCTATA
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gtttggagttcatctgg----ttttgcatttatcgttttt-ttttctctttgatgtggaattcc---------atctttgctta----------tgat--ttactactta----ccttt---ggatttttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA
upper sequence: LOC_Os02g43090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 4
gtttgggcttcaactgtattctattgcaagaatcatctgtatcattttttttgtgaggacatccaatcttggtatttctgcttggtcacatcattgataatcactaattgtgctccttttccaatccatttgttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCATATTTCAATGACCGTTCAGCTATA
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gtttggatttcatctgg----ttttgcatgtactgtctttgt-atccttgatgtggagc------acctc--catctctgctt------atgatt--tacttac--attttgattttgtt--------ttgctcgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCAAAAATGCCGGACGAAGTAAGGGCTGAGATAGGCCCGTATTTCAACGCCCGCGCAGCCATA
upper sequence: LOC_Os02g43090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 4
gtttgggcttcaactgtattctattgcaagaatcatctgtatcattttttttgtgaggacatccaatcttggtatttctgcttggtcacatcattgataatcactaattgtgctccttttccaatccatttgttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCATATTTCAATGACCGTTCAGCTATA
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--------------------------taaaaaattcctg----attttggcattgggaagagtaagttataa-atttttgttccatagccacatttatgaaaactgaatga----tttttgtgaatcatt---tgcagTGTGTGGGTGATGATGAATAAGCAGACCAGGAGATTATCAAAAATTCCAGATGCAGTTCGAGCTGAAATAGAGCCTTATTTTATGGATTCTGCTCCTATT
upper sequence: LOC_Os02g43090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S167_109V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttgggcttcaactgtattctattgcaagaatcatctgtatcattttt----tttgtgaggacatccaatcttggtatttctgcttggtcacatcattgataatcac-taattgtgctccttttccaatccatttgt----tgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCATATTTCAATGACCGTTCAGCTATA
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--gtgaatatccccaatgacctggagccctcctcgttaaaaggacacacaaagcttctcaaaaaatcta-ccatggt----ctatttttttctgttatctagaagtgcatgatggtgatattgtttaggattggttgtggtgtgcagTACATGGGTGATGATGCACAGAAAAACAAGAAAGCTTTCTAAGATGCCCGAAGAAGTCAGAGCTGAAATTTCTCCCTATTTTCTGGATAGATCGGCAATTMapped 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|58678184|gb|CK066871.1|CK066871EST: TGGCATGTTCGTGACTACAACTCTGGCCGAACAATCTTGAGAGCTACAAG TGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGA
genomic: TGGCATGTTCGTGACTACAACTCTGGCCGAACAATCTTGAGAGCTACAAGgtttgggctt ... tttgttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGA
EST:
gi|29643342|gb|CB648349.1|CB648349EST: TGGCATGTTCGTGACTACAACTCTGGCCGAACAATCTTGAGAGCTACAAG TGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGA
genomic: TGGCATGTTCGTGACTACAACTCTGGCCGAACAATCTTGAGAGCTACAAGgtttgggctt ... tttgttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcacatcattgataatcactaattgtgctccttttccaatccatttgttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCATATTTCAATGACCGTTCAGCTATA
cactaat putative branch site (score: 2)
tccattt putative PPT
attgataat 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
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gtttgggcttcaactgtattctattgcaagaatcatctgtatcattttttttgtgaggacatccaatcttggtatttctgcttggtcacatcattgataatcactaattgtgctccttttccaatccatttgttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCATATTTCAATGACCGTTCAGCTATA
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