Sequence
atgc intronic sequence ATGC exonic sequence...cgaaaatcaggaataccttcttccatggagtgttccatgctatttgccctgcatacggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g64090.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g64090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G023748_T02 (Zea mays), 3'ss of exon 3
cgaaaatcaggaataccttcttccatggagtgttcca-tgctatt--tgccctgcatacggatgctgatgtttcttttctctgttaccaatgctat----tgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT----
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-----------agtataactctccatgaaatcaacaagtgtcggtaatgccttggttgcctttgttttgatatatttgttctaatgatggtactatgctgtatgtaggcagAGAGAATAGGTATAGACAATATGGATGTGGAAGCCCTCAAGAAGATGAACAAAAACAAGAAGCTAGTGAAGAAGCTGGCAAAGAAGTACCATGCTTTCCT
upper sequence: LOC_Os01g64090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G023748_T01 (Zea mays), 3'ss of exon 3
cgaaaatcaggaataccttcttccatggagtgttcca-tgctatt--tgccctgcatacggatgctgatgtttcttttctctgttaccaatgctat----tgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
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-----atatagtataactc--tccatgaaatcaacaagtgtcggtaatgccttggttgcctttgttttgatatatttgttctaatgatggtactatgctgtatgtagGCAGAGAGAATAGGTATAGACAATATGGATGTGGAAGCCCTCAAGAAGATGAACAAAAACAAGAAGCTAGTGAAGAAGCTGGCAAAGAAGTACCATGCTT
upper sequence: LOC_Os01g64090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G08360.1 (Arabidopsis thaliana), 3'ss of exon 3
cgaaaatcaggaataccttcttccatggagtgttccatgct--atttgccctgcatacggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
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tgtagatgcatgatgttttcggaatttggtcattgtttatttaggcttcatttcttgcataattaaatatttgcttatttcat--cttgtatcttttcgtagGCTGAGAAGATGGGGTTGGAAAACATGGATGTTGAGTCTCTAAAAAAGCTTAACAAGAACAAGAAACTCGTCAAGAAGCTTGCAAAGAAATACCATGCTT
upper sequence: LOC_Os01g64090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G22440.1 (Arabidopsis thaliana), 3'ss of exon 3
cgaaaatcaggaataccttcttccatggagtgttccatgctatttgccctgcatacggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
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----------gttcacttttttccgccttttcttttgaaaatgttatgattagtacttagtagtatagtactataacttgcggttggt----ttacttagGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGAACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTT
upper sequence: LOC_Os01g64090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------cgaaaatcaggaatacct---tcttccatggagtgttccatgctatttgccctgcat---acggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
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gtatgcttattctcaaattttgattctttctatttgttgatggtgccagaaattgaataaaacattgtagaattttctgctctgggtctcatctcactggcctttgtatattaaaactagaaattatcaccctttacttgataatggataattgctgatgtcgtgagtttcttttggtcgtaactcgtcacagGCGACCAAGAATGGTATCGAGTGCATGGATGTCGAGAGCTTGAAGAAGATGAACAAGAACAAGAAACTTGTGAAGAAGCTGGCTAAGAAGTACCACGCTT
upper sequence: LOC_Os01g64090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ34353 (Selaginella moellendorffii), 3'ss of exon 2
cgaaaatcaggaataccttcttccatggagtgttccatgctatttgccctgcatacggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
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-------------------gtaagattgagcgccctgt-ctccttttgttgc---cggat-----tgaatcactggtccgttgc---tttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
upper sequence: LOC_Os01g64090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
cgaaaatcaggaataccttcttccatggagtgttccatgctatttgccctgcatacggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
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--------------------------gtaagattgagcgccctctctcctttagttgccggat--tgaatcactggtccattgct----tttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTTMapped 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|38479924|gb|CF964013.1|CF964013EST: GCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAG GCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATG
genomic: GCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAGgtattgtact ... tattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATG
EST:
gi|27920704|gb|CB096512.1|CB096512EST: GCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAG GCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATG
genomic: GCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAGgtattgtact ... tattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATG
EST:
gi|218503115|gb|FG965410.1|FG965410EST: GCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAG GCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATG
genomic: GCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAGgtattgtact ... tattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATG
EST:
gi|88202396|gb|CI201258.1|CI201258EST: CCAGCATGTTGAAGAG GCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATG
genomic: CCAGCATGTTGAAGAGgtattgtact ... tattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATG
EST:
gi|58690950|gb|CK079637.1|CK079637EST: GCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAG GCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTC
genomic: GCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAGgtattgtact ... tattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTC
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:
73 (upstream exon),
61 (downstream exon)
Score:
51TCAAAAGGATAAGCGTTTCAGTGGATCTGTTAAGTTGCCTCACATCCCCCGCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAGgtattgtact ... tattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccctgcatacggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
tgctgat putative branch site (score: 51)
tttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgaaaatcaggaataccttcttccatggagtgttccatgctatttgccctgcatacggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
-gaaaatca
- - - - - - - - - - ttccatg
- - - - - - - - - - - - - - - - -tccatgc
- - - - - - - - - - - - - - - - - - - - - tttgccc
- - - - - - - - - - - - - - - - - - - - - - - - -tgcatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat