Sequence
atgc intronic sequence ATGC exonic sequence...aaatatggaacattggaattcttgtgtgctatttaacaatgctactatttgtatttgccttttaagtttcagtgatcttatgaatcaacaatacctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g36960.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G137118_T01 (Zea mays), 3'ss of exon 11
aaatatggaacattggaattcttg-tgtgctatttaacaatgctactatttgtatttgccttttaagtttcag-tgatctta--tgaatcaacaatacctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT
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---cttggaccttttcctctcttaatataatgacgtgtagtcctcccgcgcgttcgagaaaaaaaaatttctgatgatctgacctgaattt-cattgcctgcagGATATGGCTGGATTAATAAGCAAGATAAATCGGTCTTCCATGGGTCCTTTGCCTGCCTGTTACTCAGTGTCTAT
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 10
aaatatggaacattggaattcttgtgtgct---atttaacaatgcta---ctatttgtatttgccttttaagtttcagtgatcttatgaatcaacaatacctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT
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-gttgtggcccctatcttgcctgatatatttatgtatgtgaatgtgaaggcaatttttcatcatcttttttccttgataagtgtcgtatatc-----ttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 10
-aaatatggaacattggaattcttgtgtgctatttaacaatgctactatttgtatttgccttttaagtttcagtgatcttatg----aatcaacaatac-ctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT
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tagatatagatattta----tgttatatg-tatgtggaggtatttcagcgtg-gtttatttcttgggttttaacgatgagatggcataatgaatcatatgtttcagGATATGGCAGGACTGATAAGCAAGATAAATCGTTCATCCATTGGCCCTTTGCCTCCATGTTATTCCCCTTCCTT
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 10
aaatatggaacattggaattcttgtgtgctatttaacaatgc---tactatttgt-atttgccttttaagtttcagtgatcttatgaatcaacaatacctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT
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aagcttgttgtggccccaatttggtctgatatattgatatgtgtgtgcaatttgtcatcttgtttttttttcttgataagcatg---gtaaatcttgttt-cagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
upper sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 10
aaatatggaacattggaattcttgtgtgctatttaacaatgctactatttgtatttgccttttaagttt-cagtgatcttatgaatcaacaa-tacctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT
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-tatatgtgatttta-atttgttatcacccaaatatgaattctgaaactgtttactccattttatttgtattctaacattggcattctacatctggtttcagGATATGGCTGGATTAATAAGTAAAATAAACCGTTCTTCTATTGGTCCTTTGCCCTCATGCTATTCCCCTTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttgtatttgccttttaagtttcagtgatcttatgaatcaacaatacctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT
ttttaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatatggaacattggaattcttgtgtgctatttaacaatgctactatttgtatttgccttttaagtttcagtgatcttatgaatcaacaatacctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT
- - - - - - - - -attcttg
- - - - - - - - - - - - - tgctatt
- - - - - - - - - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaca