Sequence
atgc intronic sequence ATGC exonic sequencegtaagaattcaagctatttatgtttaataactttgatgtattgtcaagtcaatatctaatgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g37120.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G106140_T01 (Zea mays), 3'ss of exon 8
gtaagaattcaagctatttatgtttaat--aactttgatgtat-tgtcaagtcaatatctaatgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC
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gtaagtagacattctatttatgttcactttaaccctactatatatgtgtagccagtttgtaatgcattcatc-cttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G141735_T01 (Zea mays), 3'ss of exon 8
gtaagaattcaagctatttatgtttaat--aactttgatgtat-tgtcaagtcaatatctaatgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC
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gtaagtagttaatctattcatgttcactttaatcctagtatatatgtatagccagtttgtaatgcattcatc-cttctacagTATGGGCATTTCTTCCCTGACCCTCAATATGAAAATGTGCAACACATCATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTGCCCATA
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G27460.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------gtaagaattcaagctatttatgtttaataactttgatgtattgtcaagtcaatatctaatgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC
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gtatgtggttttagtgaaaaccgaaagttcagataatgattttttttttttttttttttttgcttcagctaacagtttagccttacttgcagTTTGGTCACTTCTTTCCAGATCCACAGTACGAGAACCTTCAGCATATCATCTGCTGTGATTCATATGCAACATATGCATATGACTTTGAATTTGCAGATA
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv06s0080g00510.t01 (Vitis vinifera), 3'ss of exon 8
----gtaagaat-tcaagctatttatgttta--ataactttgatgta--ttgtcaagtcaatatcta-atgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC
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gtgagtgatcatatcatgtcctttaagattgtcatagctgtgttacactttgtttattttacatttacacttacattaaatttttgcagTATGGTCATTTCTTCCCAGATCCACAGTACGAAAATGTGCAACACATTATTTGTTGTGATTCTTATGTCACATATGCCTACGATTTTGATTTTGCCAACA
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ30507 (Selaginella moellendorffii), 3'ss of exon 8
gtaagaattcaagctatttatgtttaataactttgatgtattgtcaagtcaatatctaatgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC
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--------------------------gtaagtacagtgcgctg--gattcgctgactacttactttgt-gctcgtacagTATGGCCACTTCTTTTCTGATCCTCAATATGAAAATGTCCAGCATATTATCTGTTGCGATCCTCATGCAACTTACGCTTATGATTTTGATTTTGGAAATT
upper sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ23029 (Selaginella moellendorffii), 3'ss of exon 8
gtaagaattcaagctatttatgtttaataactttgatgtattgtcaagtcaatatctaatgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC
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--------------------------gtaagtacagtgcgctg--gattcgctgactacttactttgt-actcgtacagTATGGCCACTTCTTTTCTGATCCTCAATATGAAAATGTCCAGCATATTATCTGTTGCGATCCTCATGCAACTTACGCTTATGATTTTGATTTTGGAAATTMapped 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|29674495|gb|CB670770.1|CB670770EST: GTTGTGTTCTAAGGTTGAGAACATCTTCAGATTTTGAACCTGGCAATTCT TATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATC
genomic: GTTGTGTTCTAAGGTTGAGAACATCTTCAGATTTTGAACCTGGCAATTCTgtaagaattc ... atttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATC
EST:
gi|29616493|gb|CB621505.1|CB621505EST: GTTGTGTTCTAAGGTTGAGAACATCTTCAGATTTTGAACCTGGCAATTCT TATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATC
genomic: GTTGTGTTCTAAGGTTGAGAACATCTTCAGATTTTGAACCTGGCAATTCTgtaagaattc ... atttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taataactttgatgtattgtcaagtcaatatctaatgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC
tcattttt CT-rich tract
aatatctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaattcaagctatttatgtttaataactttgatgtattgtcaagtcaatatctaatgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC