Sequence
atgc intronic sequence ATGC exonic sequence...ctgatatttattttatttagggttctaagatatgtcattgccttattgatctgcctgtttaatctttctccataccttattatattttttgtaatttcagGTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCACAGTTCATACTAGAAGAGGAGATAGATAACCTTCGTGGTGCTGATTGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os10g33275.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 7
--ctg-atatttattttatttagggttctaagatatgtcattgcc-ttattgatctgcctgtttaatctttctccataccttattatattttttgtaatttcagGTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCACAGTTCATACTAGAAGAGGAGATAGATAACCTTCGTGGTGCTGATTGTA
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gattgcatgtttaggttgtgtatctgtataattt-tagaattgctgttattagtgtgggtatttttttccactcttaacttgttgagttttcctgta---tcagGTTCTGGTCATTTCTGGCGAGACAGGCTGCGGCAAAACAACTCAGCTTCCACAGTTCATTCTAGAAGAAGAAATAAACAGCCTCCGCGGTGCTGATTGCA
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 7
ctgatatttattttatttagggttctaagatatgtcattgccttattgatc-tgcctgtttaatc--tttctccataccttattatattttttgtaatttca--gGTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCACAGTTCATACTAGAAGAGGAGATAGATAACCTTCGTGGTGCTGATTGTA
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----tatttgactgtttttgaattatcatcaattgcagt-tattattggttatagttatatctttggttcttcaacagcataaaatttggcttgtgtttgcacagGTATTAGTAGTTTCAGGAGAGACAGGTTGTGGTAAAACAACACAGTTGCCACAATTCCTTCTGGAAGAAGAAATATCTTGTTTGCGCGGAGCTGATTGCA
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 5
ctgatatttattttatttagggttctaagatatg-tcattgccttattgatctgcctgtttaatctttctccataccttattatattttttgtaatttcagGTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCACAGTTCATACTAGAAGAGGAGATAGATAACCTTCGTGGTGCTGATTGTA
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tttatgactgtttc-tgaattatcatcaattgcaatcattattggttatagttatatctttgattttgcaacagcgtaaaatttggcttgtgtttgcacagGTATTAGTAGTTTCAGGAGAGACGGGCTGTGGTAAAACAACACAGTTGCCACAATTCATTCTAGAAGAAGAAATATCGTGTTTGCGCGGAGCTGATTGCA
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 5
ctgatatttattttatttagggttctaagatatgtcatt--gccttattgatctgcctgtttaatctttctccataccttattatatttt-ttgtaatttcagGTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCACAGTTCATACTAGAAGAGGAGATAGATAACCTTCGTGGTGCTGATTGTA
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--aatttccaatgaagttttcccttttagctaaattttctggtcgtcattaatagcacatattat-tctcactgattctcattatttttgatcgaggatatagGTACTGGTAGTTTCAGGGGAGACAAGTTGTGGTAAAACGACACAGCTCCCTCAGTTTATCCTAGAGGAGGAGATATCATCTCTTCGAGGTGCTGATTGTAMapped 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|58606624|gb|CK034657.1|CK034657EST: CAGCATTCAAAATGAGAGAGGAGTTTTTGAAAGCAGTAGCAGCCAATCAG GTTCTAGTAATTTCTGGTGAGACAGGCTGCGGTAAAACAACACAGCTTCCA
genomic: CAGCATTCAAAATGAGAGAGGAGTTTTTAAAAGCAGTAGCAGCCAATCAGgtaagaaaca ... gtaatttcagGTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCA
EST:
gi|33678639|gb|CF306878.1|CF306878EST: CAGCATTCAAAATGAGAGAGGAGTTTTTAAAAGCAGTAGCAGCCAATCAG GTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCA
genomic: CAGCATTCAAAATGAGAGAGGAGTTTTTAAAAGCAGTAGCAGCCAATCAGgtaagaaaca ... gtaatttcagGTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatctgcctgtttaatctttctccataccttattatattttttgtaatttcagGTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCACAGTTCATACTAGAAGAGGAGATAGATAACCTTCGTGGTGCTGATTGTA
ttttttgt CT-rich tract
ataccttattatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgatatttattttatttagggttctaagatatgtcattgccttattgatctgcctgtttaatctttctccataccttattatattttttgtaatttcagGTTCTAGTAATTTCTGGTGAGACAGGCTGTGGTAAAACAACACAGCTTCCACAGTTCATACTAGAAGAGGAGATAGATAACCTTCGTGGTGCTGATTGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT