Sequence
atgc intronic sequence ATGC exonic sequencegtctttactcataatccatctaggtaattattgtgcatgagtagttgagttgtttattatgacctgacaagcttgttttcattgtgtagAATGTACCACCTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTGCGTTGAGGGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g43930.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g43930.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 4
gtctttactcata---atcca-tctaggtaattattgtgca-tgagtagttga-gttgtttattatgacc-tgacaagcttgttttcattgt------gtagAATGTACCACCTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTGCGTTGAGGGCTA
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gtctgtacacctatccatccagtttcagcgacagttatgcactttatgtttgatgttatataacctgattataacaaatatgttatgactgtctctatgtagAATGTGCCACCTGCCCTACTAGTACGATTTCTGAGGGAGCATCGCTCCGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCCGCTGCTCTTAGGGCTA
upper sequence: LOC_Os03g43930.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------------gtctttactcataatccatctaggtaattattg-tgcatgag---tagttgagttgtttattatgacctgacaa-gcttgttttcattgtgtagAATGTACCACCTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTGCGTTGAGGGCTA
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gtacatgaaacagttctatggactatgacataatataatattaataatattaataatttcaatgccaaattcctctttttgtttcccaattcgtgaagcatcttctaaattttctctataatcatctattgtacaatgtgtctctacagAATGTTCCCCCTGCTTTGCTTGTTCGATTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCTGCATGCCTTAAAGCTA
upper sequence: LOC_Os03g43930.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------------------------------------------------gtctttactcataatccatctaggtaattattgt--gcatgagtagttgagttgtttattatgacctgacaagcttgttt---tcattgtgtagAATGTACCACCTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTGCGTTGAGGGCTA
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gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacatcacta-ttgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTAMapped 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|58673031|gb|CK061717.1|CK061717EST: TGCAATTGGAGGCGGCATCTTGTGTTGCAAAGGCATCTATGCTGTTACAG AATGTACCAACTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAA
genomic: TGCAATTGGAGGCGGCATCTTGTGT-GCAAAGGCATCTATGCTGTTACAGgtctttactc ... cattgtgtagAATGTACCACCTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatgagtagttgagttgtttattatgacctgacaagcttgttttcattgtgtagAATGTACCACCTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTGCGTTGAGGGCTA
acctgac putative branch site (score: 3)
cttgttttc putative PPT
ttgtttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctttactcataatccatctaggtaattattgtgcatgagtagttgagttgtttattatgacctgacaagcttgttttcattgtgtagAATGTACCACCTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTGCGTTGAGGGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC