Sequence
atgc intronic sequence ATGC exonic sequencegtatttatcttggatccacactagtcgagaaacaatggatattgctgttcttggttctcgtgctctgatccatttggcaaaattttactgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g29390.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 6
gtatttatcttggatccac--actagtcgagaaacaatggatattgctgttcttggttctcgtgctctgatccatttggcaaaattttactgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA
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atcccttccctagacccccccactcatgtgggagcctttggccctggatctacctttttttctgttcttgatatctaatccacctggccatcttttctagTGTTGGCTTGGCACACAGGGAGGAAGGTGATTTAGGTCCAATTTATGGATTTCAGTGGCGTCACTTTGGTGCTGA
upper sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 5
gtatttatcttggatccacactagtcgagaaacaatggatattgctgttcttggttctcgtgctctgatccatttggcaaaattttactgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA
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gtatttatc--agttggatataagctgtaaataaat---tatt-----tctctgttattgatatctaatccacctggtcatctttt--------ctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
upper sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatttatcttggatccacactagtcgagaaacaatggatattgctgttcttggttctcgtgctctgatccatttggcaaaat-tttactgtgttct-agTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA
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gtaat-atttgtaacctgcattatctttttggttaaaga-aatattgatcttgac-----------gacctatttgctgatttatccaccgtattttcagTATCGGCCTGACAGAGAGAGAGGAAGGCGACCTTGGACCTGTATACGGATTTCAATGGCGACACTTTGGTGCTAA
upper sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatttatcttggatccacactagtcgagaaacaatggatattgctgttcttggttctcgtgctctgatccatttggcaaaattttactgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA
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--gtaaactttaattcagcatttttctttcacaacttgaagct-----ttgtggccat--tacactgataaatt--gaaagttttta----atttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAAMapped 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|58679565|gb|CK068252.1|CK068252EST: AAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAG TGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAGgtatttatct ... tgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATT
EST:
gi|29626373|gb|CB631384.1|CB631384EST: AAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAG TGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAGgtatttatct ... tgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATT
EST:
gi|58685747|gb|CK074434.1|CK074434EST: AAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAG TGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAGgtatttatct ... tgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATT
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:
62 (upstream exon),
60 (downstream exon)
Score:
16GTTTTACAAGAGAAAGGCATTCATATTTGGGATGGCAATGCTTCGAGAGAGTATCTTGACAGgtatttatct ... tgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgttcttggttctcgtgctctgatccatttggcaaaattttactgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA
ctctgat putative branch site (score: 16)
ttttact putative PPT
aaaattttact TA-rich tract