Sequence
atgc intronic sequence ATGC exonic sequence...actcatacacggatgacgtaccaaaataccagcaaaaacatcttcaatttttataatagtagagatatggaagtatattcatagcaattgacttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32570.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G057504_T01 (Zea mays), 3'ss of exon 6
-actcatacacggatgacgtac-caaaataccagcaaaaacatcttcaatttttataatagtagagatatggaagtatattcatagcaattgacttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG
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ggatgtcacgcagagcagttccgccgattagttttaccatagtttgcgagatctgatctgttgaaaatgtt--aggactttcattgcacttgacctatgcagGTTCTGCTTATGTCTCTGAAGGCTGGAGGTGTTGGAATCAATCTTACTGCCGCTTCTAATGCATTTGTCATG
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA17G05390.1 (Glycine max), 3'ss of exon 17
actcatacacggatgacgtaccaaaataccagcaaaaacatcttcaatttttataatagta-gagatatggaagtatattcatagcaattgacttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG
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-gtcttg-acatacttcctcttgcatttgtttgtgacctagacagtgtagtgaaactggttcgatgcattga-gtat-ttgatacttatttcttgcatcagGTGCTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 18
actcatacacggatgacgtaccaaaataccagcaaaaacatcttcaatttttataatagtagagatatggaagtatattcatagcaattgacttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG
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-gtcttg-acatacttcctctcgcatttgtttgtgacctagacagtgtagttaaactggttcaatgcattgactatgca-atacttatttcttgcatcagGTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATG
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G22750.1 (Arabidopsis thaliana), 3'ss of exon 17
actcataca--cggatgacgtaccaaaataccagcaaaaacatcttcaatttttataatagtagagatatggaagtatattcatagcaattgacttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG
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gttggtgcagtcgcattacattgcaatgt-tcaatacttatactttctagtttcgaaattgaag-----ttaaaaagtctccttttcaattg--ttggatagGTACTGTTGATGTCTCTAAAAGCTGGTGGCGTTGGGATAAATCTAACAGCTGCGTCCAATGCTTTTGTCATG
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 3'ss of exon 17
---------------------------------actcatacacggatgacgtaccaaaataccagcaaaaacatcttcaatttttataatagtagagatatggaagtatattcatagcaattgacttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG
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gtttgtcagaaaaaatgtggccttttttttttgtccctttctctgaaga-gaaaggaggtgtggggaagagagggtttgggtttaatagttg-----------acgcacatttttggtgtttg--ttacatagGTCTTGCTAATGTCGTTGAAGGCTGGTGGAGTTGGAATAAACCTAACGGCTGCATCCAATGCCTTTGTTTTGMapped 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|88197570|gb|CI197420.1|CI197420EST: GCAGAGAGAGAAAGTAATCCAAGGAGTTTTCTGAGGACAAAAGCATTTTG GTTCTGCTTATGTGCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCT
genomic: GCAGAGAGAGAAAGTAAT-CAAGGAGTTTTCTGAGGACAAAAGCATTTTGgtatgctctt ... acttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCT
EST:
gi|86479033|gb|CI121666.1|CI121666EST: AGCAGAGAGAGAAAGTAATCAAGGAGTTTTCTGAGGACAAAAGCATTTTG GTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCT
genomic: AGCAGAGAGAGAAAGTAATCAAGGAGTTTTCTGAGGACAAAAGCATTTTGgtatgctctt ... acttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttttataatagtagagatatggaagtatattcatagcaattgacttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG
aattgac putative branch site (score: 3)
ttataatagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actcatacacggatgacgtaccaaaataccagcaaaaacatcttcaatttttataatagtagagatatggaagtatattcatagcaattgacttatgcagGTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC