Sequence
atgc intronic sequence ATGC exonic sequenceGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgcagagtccactagactttacactaagctgccaaacgatgaaccatgctgattttcctccttctctccag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g13590.1 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM5G823484_T01 (Zea mays), 5'ss of exon 3
GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgcagag-tccactagactttacactaagctgccaaacga------tgaaccatgctgattttcctccttctctccag---
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CAAGAGGTGGCAGCTTCAGCTGGTGAGAGCAGCTTTAGATCCTTTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAGgtaatcttcgctgatccatcaagttgcaaccttggcttgcatatgaagtcaataaagcatgcttgaatttctctgtttcctctgtag
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA07G05160.1 (Glycine max), 5'ss of exon 17
GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgcagagtccac-----tagactttacactaagctgccaaacgatgaaccatg-ctgattttcctccttctctccag
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GCAGAGGCGGCAGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTTATGATTGCTGTACAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAAgtacaatattgagcctttatttttaattaatattttttgctat-aaacaaaaccctatggctgaaatgagtaattttctgcag
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA16G01660.1 (Glycine max), 5'ss of exon 17
GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgcagagtccactagactttacactaag-----ctgccaaacgatgaaccatg---ctgattttcctccttctctccag
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GCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATTGCTGTGCAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAAgtacaatattgagcc---ttgatttttaattaatattttttgctataaacaaaaccctataactgaaatgagtaattctctgcag
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 5'ss of exon 17
GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgcagagtccactagactttacactaagctgccaaacg-atgaaccatgctgattttcctccttctctccag------------------------
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GCAGAAGCTGCTGCTGCTGCTGGTGAAAGCAGTTTCAGATCTTTCATGGTGGCTGTACAGCGTTGTGCTAGCAGTGTGGCTATTGTTCAGCAAgttcgttagatggccgaatgccttttactcaattattttaattatgctcatgagaatgattagaaatttattttgaaataaattggactgctttttctgcagMapped 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|33822211|gb|CF336920.1|CF336920EST: ATGANTTGCTGTGCNAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG TACTTCTCAAATACTATATCTCGGCTCCTGCTNGCCTGTGGATGGTGCCCA
genomic: ATGA-TTGCTGTGC-AGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgca ... ttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCT-GCCTGTGGATGGTGCCCA
EST:
gi|29669745|gb|CB666020.1|CB666020EST: TCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG TACTTCTCAAATAATATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCAC
genomic: TCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgca ... ttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCAC
EST:
gi|33822202|gb|CF336916.1|CF336916EST: TCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG TACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCAC
genomic: TCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgca ... ttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCAC
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:
52 (upstream exon),
68 (downstream exon)
Score:
21GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAGgtaatatgca ... ttctctccagTACTTCTCAAATACTATATCTCGGCTCCTGCTGCCTGTGGATGGTGCCCACCCCTCAGCTTGTGAAGATATGGGATCAGCAGTATCTGTTGTTGAGGCTG
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