Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgactagaagttactataattggcattcataaacgttgctttgtgacctgaaacatgtgttacaattactgtttttgacttccttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTTCTTGGATTTATTGATGATGTTCTTGATGTTCCATGGAGAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g46640.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G827205_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------gtatgttgactagaagttactataattggcattcataaacgt-tgctttgtgacctgaaacatgtgttacaattactgtttttgacttccttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTTCTTGGATTTATTGATGATGTTCTTGATGTTCCATGGAGAGT
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gtatgcagtgacgagcagtattttttaacatttacaaactactccctccgttcttttttatttgtcgccggcgaaaaaattcgagaacggaggtagtatgtcttatgtcctgaaacatgtttcacagttgtttttgttgtcttc-ttgttgcagTGGCTTGTTGAATATAATGCAGCATTGACATCCATCTGCTTTATGATTCTTCTTGGATTTGTTGATGATGTTCTTGATGTTCCATGGAGAGT
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 2
gtatgttg--actagaagttactataattggcattcataaacgttgctttgtgacctgaaacatgtgttacaattactgtttttgacttccttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTTCTTGGATTTATTGATGATGTTCTTGATGTTCCATGGAGAGT
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gtatgctgtgaccaccagt-atttt--tttacacttacaaac----tgttatgtcctgaagcatatttaacagtggcttttgctgtcttcttt-ttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgttgactagaagttactataattggcattcataaacgttgctttgtgacctgaaacatgtgttacaattactgtttttgacttccttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTTCTTGGATTTATTGATGATGTTCTTGATGTTCCATGGAGAGT
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-----gtaagtgtgcattaacgt--cttgttttattaatctctg--tggttattctcattatcaatgtttgtgagtctggctgatgattctgt-gcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 2
--gtatgttgactagaagttactataattggcattca--taaacgttgctttgtgacctgaaacatgtgttacaattac--tgtttttgacttccttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTTCTTGGATTTATTGATGATGTTCTTGATGTTCCATGGAGAGT
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atttaagttagctaagccctaggttagttaggtctgactttgaagacattttcttcttttaac----ttttagaattaaaatgttgactacttcattcatgcagTGGCTTGTTGAGTACAATGCAGCCTTAGCATCCATCTGCTTCATGACCCTGCTTGGATTTGTAGATGATGTTCTTGATATTCCATGGAGAGTMapped 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|38473384|gb|CF957516.1|CF957516EST: TGGTCATTGCTATTCTATTTCAACATTTCAACTTCACAGCAGACTCTATG TGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTT
genomic: TGGTCATTGCTATTCTATTTCAACATTTCAACTTCACAGCAGACTCTATGgtatgttgac ... cttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttgtgacctgaaacatgtgttacaattactgtttttgacttccttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTTCTTGGATTTATTGATGATGTTCTTGATGTTCCATGGAGAGT
ttttgac putative branch site (score: 3)
tttttgacttcctt CT-rich tract
ttacaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgactagaagttactataattggcattcataaacgttgctttgtgacctgaaacatgtgttacaattactgtttttgacttccttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTTCTTGGATTTATTGATGATGTTCTTGATGTTCCATGGAGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA