Sequence
atgc intronic sequence ATGC exonic sequence...ttcacttccatgcatatctggatcttttatacaaatatattttcccatctatatgatgtaaagattaaaatagtttctataacaccatttgcatattcagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g42410.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
ttcacttccatgcata--tctggatcttttata-caaatatattttcccatctatatgatgtaaagattaaaatagtttctataacaccatttgc-atattcagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG
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aacaataatgtttgttattctctatctttgagaatatgaatactgtcgaatccgtatgctggcaa----acaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
ttcactt-ccatgcatatctggatcttttatacaaatatattttcccatctatatgatgtaaagattaaaatagtttctataacaccatttgcatatt-cagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG
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tccagttatcgtacactttatcttctttcggacat-taaagtgcactaaagttctaat-tatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG
upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 7
ttcacttccatgcatatctggatcttttatacaaatatattttcccat--ctatatgatgtaaagattaaaat--agtttctataacaccatttgcatatt------cagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG
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----------gacctaatttggtatatgatgaaaatgtgtttttgtattacttcttcattgtaggatctctttttggtgaatatgatctcatttttggatttttttgcagGCAATTGACCACATCATTAATTCTGCTGCAAAATCAAACTACATGTCCGCTGGTCAGATATCCGTACCTATTGTTTTTAGAGGACCAAATGGTGCTGCCG
upper sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
----ttcacttccatgcatatctggatcttttatacaaatatattttcccatctatatgatgtaaagattaaaatagtttctataacaccatttgcatattc-agGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG
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gtagattccgttagtgaacatttggtttttttttcc---ttaactttttactttttatttttttatttttccttt--ttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTGMapped 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|428335|gb|D24483.1|D24483EST: AAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG GCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCT
genomic: AAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtcaatcatt ... gcatattcagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCT
EST:
gi|218484233|gb|FG953202.1|FG953202EST: AAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAG GCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCT
genomic: AAGGTCTTCGCCCTGTGGTTGAGTTCATGACATTTAACTTCTCTATGCAGgtcaatcatt ... gcatattcagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctatatgatgtaaagattaaaatagtttctataacaccatttgcatattcagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG
ctataac putative branch site (score: 3)
atgtaaagattaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcacttccatgcatatctggatcttttatacaaatatattttcccatctatatgatgtaaagattaaaatagtttctataacaccatttgcatattcagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT