Sequence
atgc intronic sequence ATGC exonic sequencegtaacttacctatccgtcatcctccatacatgttttaattaatatgctggagaaaggtgatctatcgtttagcttatgactggctttatgcaatcattcataagcttgatatgttaacattgtaacccctgcactagGTGACTGGCATGGAACCATCAGATGAACCAGTTCATCGCGTCAACTGTAATCAAACAGCCCTTGTTCTTGGGGGAGGTGCTTCTGCTTCAATACCCCCTT
Basic information
| species | Oryza sativa |
| transcript | LOC_Os04g52690.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52690.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 3
gtaacttacctatccgtcatcctccatacatgttttaattaatatgctggagaaaggtgatctatcgtttagcttatgactggctttatgcaatcat-------------tcataagcttgata------tgttaacattgtaacccctgcactagGTGACTGGCATGGAACCATCAGATGAACCAGTTCATCGCGTCAACTGTAATCAAACAGCCCTTGTTCTTGGGGGAGGTGCTTCTGCTTCAATACCCCCTT
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---gtatacctatgtttcatacttaaaat-tactttagtccataagttcttcactggcaattgaacttatagctcatatctaactgcatttgctcataattgtaactattttataggattgctgcttgtttgttgatattttaattaat-tgttagGTGACTGGCATGGAACCATCAGATGAACCTATACTTCGTGTTAATTGCAATGAAACAGCCCTTGTACTTGGTGGAGCTGCTTCTGCTGCAATCCCCCCTT
upper sequence: LOC_Os04g52690.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 3'ss of exon 2
gtaacttacctatccgtcatcctccatacatgttttaattaatatgctggagaaaggtgatctatcgtttagcttatg-actggct--ttatgcaatcattcataagcttgatatgtta---aca--ttgtaacccctgcact-agGTGACTGGCATGGAACCATCAGATGAACCAGTTCATCGCGTCAACTGTAATCAAACAGCCCTTGTTCTTGGGGGAGGTGCTTCTGCTTCAATACCCCCTT
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-----gtaaatatctccctttttccccaaatgttct----cctatgctcaaggaatgtcattacacaaacacattctacattggctgttcatgtcttctacaactggctgttcatgtcctctacaactggctgttcatgtcctcagGTTGTGGCTATGGAACCAGCAGATGAACCAGTTCTTCGAGTTAATTGCACTCAAACTGCCCTTGTGCTTGGAGGAAGTGTTCCATCAGCTGTTCCACCTGMapped 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|29667675|gb|CB663950.1|CB663950EST: GCAACAGGGAGGACAATAGACTCCATCCTCATGATATGATTTACTTCAAG GTGACTGGCATGGAACCATCAGATGAACCAGTTCATCGCGTCAACTGTAAT
genomic: GCAACAGGGAGGACAATAGACTCCATCCTCATGATATGATTTACTTCAAGgtaacttacc ... cctgcactagGTGACTGGCATGGAACCATCAGATGAACCAGTTCATCGCGTCAACTGTAAT
EST:
gi|29626782|gb|CB631793.1|CB631793EST: GCAACAGGGAGGACAATAGACTCCATCCTCATGATATGATTTACTTCAAG GTGACTGGCATGGAACCATCAGATGAACCAGTTCATCGCGTCAACTGTAAT
genomic: GCAACAGGGAGGACAATAGACTCCATCCTCATGATATGATTTACTTCAAGgtaacttacc ... cctgcactagGTGACTGGCATGGAACCATCAGATGAACCAGTTCATCGCGTCAACTGTAAT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
37 (upstream exon),
73 (downstream exon)
Score:
4TTTTTGCATAAGGAACAATTGGAATTGTGGCGCAACCTCCTGCCTTGCATGCAACAGGGAGGACAATAGACTCCATCCTCATGATATGATTTACTTCAAGgtaacttacc ... cctgcactagGTGACTGGCATGGAACCATCAGATGAACCAGTTCATCGCGTCAACTGTAATCAAACAGCCCTTGTTCTTGGGGGAGGTGCTTCTGCTTCAATACCCCCTT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttatgcaatcattcataagcttgatatgttaacattgtaacccctgcactagGTGACTGGCATGGAACCATCAGATGAACCAGTTCATCGCGTCAACTGTAATCAAACAGCCCTTGTTCTTGGGGGAGGTGCTTCTGCTTCAATACCCCCTT
ttgtaac putative branch site (score: 4)
cccctgc CT-rich tract
atatgttaa TA-rich tract
