Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattttttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataatttatttctgcaaaacgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g38590.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G124918_T01 (Zea mays), 3'ss of exon 8
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcatttt--ttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataatttatttctgcaaaacgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
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---------------gtaaatgcaatagattaaatcgtttcctccctatgaatattacagttattatatctctacttggtgagctccccgtaaaattattatccactataccgtgcatgtgt--------ttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG
upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G011078_T01 (Zea mays), 3'ss of exon 8
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattttttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataa-tttatttctgcaaaacgtat-cacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
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-----------------------------------------gtaaatgcgatgatacccac--aagtcgtttcctcccta----caaataacatttcactctcatataagtttctgtctgcaacacatgtgtgcagGAACGAGAGCGCTCTCAAGTTCGGATGGTTTTTCCTCTTCTACTTG
upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 8
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattttttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataatttatttctgcaaaacgtatca-cagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
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----------------------------attgaa----gcattcatgagaacaataggcaaatatgcatgcatattttcatctt---tttattttgccttactgttgatcttgaatatgctgctctttttttcagGAATGAAAGTGCTTTGAAATTTGGATGGTTTTTCCTGTTTTATCTG
upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 7
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattt--tttgtgaggttttctgttgtttagttcgaactaatatctc--cttggctcataat-ttatttctgcaaaacgtatc-acagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
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----------------------------------------acctctggtactcaattaatatataatatttatttttgctgagcaaaaaaaaaaaatttggtcttactgttgatcttgaatatgctgttcttttttgcagGAATGAAAGTGCTTTGAAATTTGGATGGTTTTTCATGTTTTATCTG
upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 8
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcattttttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataatttatttctgcaaaacgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
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-----------------------------ccaccatccatatgtgt--gtgtgcatgtatgtttgtatgtgtgtt-tatggttttacctgacaattttctgttatctgatca--cactacaacatttcttacagGAATGAAAGTGCTTTGAAGTTTGGATGGTTTTTCATGTTTTATTTGMapped 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|29662769|gb|CB659044.1|CB659044EST: CGACCACTTTACCGTGCCATGAG GAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCGGTTCTACTGG
genomic: CGACCACTTTACCGTGCCATGAGgtaaatgaaa ... cgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
EST:
gi|25799630|gb|CA755591.1|CA755591EST: TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAG GAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
genomic: TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAGgtaaatgaaa ... cgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
EST:
gi|29662682|gb|CB658957.1|CB658957EST: TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAG GAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
genomic: TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAGgtaaatgaaa ... cgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
EST:
gi|29662718|gb|CB658993.1|CB658993EST: TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAG GAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
genomic: TGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAGgtaaatgaaa ... cgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
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:
71 (upstream exon),
34 (downstream exon)
Score:
2GTCCCAAGATCTGGTTTCTTGCTGTCATCTATTTCATTCTTGGATGCCCAGGTGCCTACTATCTGTGGTACCGACCACTTTACCGTGCCATGAGgtaaatgaaa ... cgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttcgaactaatatctccttggctcataatttatttctgcaaaacgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
aactaat putative branch site (score: 2)
tcataatttatttct TA-rich tract