Sequence
atgc intronic sequence ATGC exonic sequence...ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g07830.3 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 9
ttgactgttcttatccaattggtgcgtaaaatcc--ccagatgtgtttgtttat-ccagtgagagtgtgatgcttcttagctaatttg-ttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
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--tgctattttttcc--attggctggtaccgttcagtgtgtactgcctactactgctggtgtagctacaatcggtcatatctgatttgcttttatatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTGCAAGTCCTTGCAAGGATCAGAGGATATGCAGATGCGGCTCAA
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 9
ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtt-tatccagtgagag--tgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
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---tgtgtctatttttagctgacaagtactgtccggtgtactgcctactatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 7
ttgactgttcttatccaattggtgc-gtaaaatcc-ccagatgtgtttgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
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-tgtctatttttagctgaccagtactgtccagtgtactaactactattgcttgtctagccttc-tgctaccacttatatctgatttgctttatatcgttcagTGATGGAGCTGCTGCATTAGCTTTGGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTGCAAGTCCTTGCAAGGATCAAAGGATATGCTGATGCAGCTCAA
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 8
ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatgg---aacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
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-aatatgtgggttttaaactctcaaatgctattaattgacatagtttgacatt-agtgatta-gccctggtttttaataaaatgaaaatgctcttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAGMapped 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|33678061|gb|CF306300.1|CF306300EST: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
agctaat putative branch site (score: 3)
taatttgttttacat 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 |
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ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA
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