Sequence
atgc intronic sequence ATGC exonic sequencegtacttatgcagagcattttttaaaaaggaaactgaactcaactttagtgtgtacaatactatcattaaccattttaaactagAAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g26870.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G377595_T01 (Zea mays), 3'ss of exon 6
gtacttatgcagagcattttttaaaaagga--aactgaactcaactttagtgtgtacaatactatcattaac--cattttaaactagAAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG
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gtacaaatctacc-tgtctaataagtaagagcaaattaatgcatttttagtgggtgcaccattaaccttaataatattctaaagtagaaacctcctacactgcagGTCAATGATCCTACAGACAACACCACCTTCGATCTTCGGCCTTCAGATGCCATAAACACTGCTGTTCGTTGCAAG
upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G006468_T03 (Zea mays), 3'ss of exon 6
gtacttatgcagagcatt--ttttaaaaaggaaactgaactcaactttagtgtgtacaatactatcattaaccattttaaactagAAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG
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gtaccaatctagttgactgatctgtaagaacaaact-aatgcattttcagtgggtagaccattgacattaa------taaagtagaaacatccggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG
upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G053531_T02 (Zea mays), 3'ss of exon 6
gtacttatgcagagcattttttaaaaagga--aactgaactcaactttagtgtgtacaatactatcattaac--cattttaaactagAAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG
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gtacaaatctacc-tgtctaataagtaagagcaaattaatgcatttttagtgggtgcaccattaaccttaataatattctaaagtagaaacctcctgcactgcagGTCAATGATCCTACAGACAACATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG
upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0001g12960.t01 (Vitis vinifera), 3'ss of exon 7
--gtacttatgcagagcatttt-ttaaaaaggaaactgaactcaactttagtgtgtacaatactatcattaaccattttaaactagAAACTGCCTATAC-TGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG
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gcatattcctgctgtaccccttgttctttaattgattgccttgtacttcatta-----gaggatacaggtgatcaatt--gacatgatgttggatgtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGMapped 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|88217099|gb|CI216948.1|CI216948EST: AACTGTTTCTGACGAAG AAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGAT
genomic: AACTGTTTCTGACGAAGgtacttatgc ... tttaaactagAAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaactgaactcaactttagtgtgtacaatactatcattaaccattttaaactagAAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG
cattaac putative branch site (score: 2)
ccatttt CT-rich tract
attaaccattttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttatgcagagcattttttaaaaaggaaactgaactcaactttagtgtgtacaatactatcattaaccattttaaactagAAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT