Sequence
atgc intronic sequence ATGC exonic sequence...gaccaaatagaccaaattaactatcaatatccatatttcatatacgttagctactaggcattgtgttaagctatggaactgattttgtttgttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g39640.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 5
gaccaaatagaccaaattaactatcaata---tccatatttcatatacgttagctactaggcattgtgttaagctatggaactgattttgttt--gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
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-----tctaagtcaccttagcagtgaatacattcgacaattaaaagtatatgatgatcaagggttgttaaatcaccttagcctgatttttatctaattttcacagTTTCCCAATTGATGAACAAATGAATATGAAATCTGTCGTGGAGTACTTCAAGGAAATGTATGGTTTCACCATTCAGCATCCTCATCTTCCTTGCCTTCAG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G079080_T01 (Zea mays), 3'ss of exon 6
---gaccaaatagaccaaattaactatcaatatccatatttcatatacgttagctactaggcattgtgttaagctatggaactgattttgtttgttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
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tagcagtgaatacattcgacaaataaaatatgtg-atggtgaaaggttgttgaacattgatgcctaaatcagttgatcg--ttttttttcctgtttttcacagTTTCCCGATTGATGAACAAATGAATATGAAATCTGTCGTGGAATACTTCAAGGAAATGTATGGTTTCACCATTCAGCATCCTCATCTTCCCTGCCTTCAG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G21450.1 (Glycine max), 3'ss of exon 7
---gaccaaatagaccaaattaactatcaatatccatatttcatatacgttagctactaggcattgtgttaagctatggaactgattttgtttgttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
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gtatgtcttttaactttagctggctg--aacttttacaatttacacaaatc--ctcctttgaaatgattttctcttc----tttttttctccccattgaacagTTTCCCTCTCGATGAGCAAATGAACATGAAATCAGTAGTTGATTATTTTCAAGAAACGTATGGATTTACTATCAAATATTCTCATCTGCCTTGTCTTCAA
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 6
gaccaaata-gaccaaattaactatcaatatccatatttcatatacgttagctactaggcattgtgttaagctatggaactgattttgtttgttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
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------gtatgtcttttttaactttagaaggttgaacttt---tacattttacacatgccctcttttgaaatgattg---tctcttttccccattgaacagTTTCCCTCTTGATGACCAAATGAACATGAAATCAGTAGTTGATTATTTTCAAGAAATGTATGGATTTACAATCAAATATTCTCATCTACCTTGCCTTCAA
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 6
-----gaccaaatagaccaaattaactatcaatatccatatttcatatacgttagctactaggcattgtgttaagctatggaactgattttgtttgttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
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gtactgatattttgtattttgccttcttttaattgtcctttttttttttttttaatcttttgaagtgagtttaagtggtgg-----tttcttctcattccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAAMapped 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|29667767|gb|CB664042.1|CB664042EST: CAACACAACCACCTCATGAACTGAT TTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCCA
genomic: CAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA
EST:
gi|58664728|gb|CK053414.1|CK053414EST: CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGAT TTTCCCAATCGATGACCAAATGAACATGAAATCTGCCGTAGAGTATTTCAA
genomic: CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA
EST:
gi|29636940|gb|CB641949.1|CB641949EST: CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGAT TTTCCCA-TCGATGACCAAATGAACATG
genomic: CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATG
EST:
gi|58662235|gb|CK050915.1|CK050915EST: TGACAACACAACCAACTCATGAACTGAT TTTGCGAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA
genomic: TGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA
EST:
gi|29636971|gb|CB641980.1|CB641980EST: CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGAT TTTCC-AATCGATGACCAA-TGAACATGAAATCTGTCGTAGAGTATTTCAA
genomic: CGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAA
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),
70 (downstream exon)
Score:
10AAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATGAACTGATgtatgttata ... gttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttagctactaggcattgtgttaagctatggaactgattttgtttgttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
aactgat putative branch site (score: 10)
tttgtttt putative PPT
attttgtttgttttaa 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 |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaccaaatagaccaaattaactatcaatatccatatttcatatacgttagctactaggcattgtgttaagctatggaactgattttgtttgttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
gaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - agctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtgtt