Sequence
atgc intronic sequence ATGC exonic sequencegtgaatacaggagtagatttgactgtccatataattgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcagAACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCGTGGAGGAACTGGTCTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32570.2 |
intron # | 3 |
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 3
lower sequence: GRMZM2G015190_T01 (Zea mays), 3'ss of exon 10
gtgaatacaggagtagatttgactgtccatataa-------ttgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcagAACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCGTGGAGGAACTGGTCTTT----
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gtgagaatatgtgtagatctatcggtctttgttagaattccctgaacatatcatgtttatccctaatgc-----aggattatggagccgacattt--------tactcttatttttcacgcatgtatttgcgtactaggtgcttatgcattcaaa----tttatgaagtttactttactcacagAACAATTTGGAGGATTTATACAGCCTTTTCCGGTTTCTGAAAGTTGAACCATGGAGGAACTGGGCTTTGTAA
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G22750.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgaatacaggagtagatttgactgtccatataattgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcagAACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCGTGGAGGAACTGGTCTTT
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---------------------------------------------------------tgctggcatgata-tcttggttcattcaaatggatggtgaa----tagta-------attttttgtcctatttggaactt-tgtgatca-----tttcac--atgttatcttattgacagAACAATCTGGAGGATTTATACAGCCTTCTACGGTTTTTGAGGATTGAACCATGGGGAACTTGGGCATG
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 3'ss of exon 10
gtgaatacaggagtagatttgactgtccatataattgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagtt-ttactctgatggcagAACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCGTGGAGGAACTGGTCTTT
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-------------------------------------------------------------------------cctaaatagtttgaaggaatttgtactacttgcaagt-tacatccgatggattttt----gtctttgcagctgttattccttgacatttattttttccatcacagAACAACCTGGAGGACATTTACAGCCTTCTTCGGTTTTTGAGGGTGGAACCTTGGGGAAACTGGGCATGMapped 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|66917088|gb|CX103936.1|CX103936EST: TTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAG AACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCG
genomic: CTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAGgtgaatacag ... ctgatggcagAACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcagAACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCGTGGAGGAACTGGTCTTT
ctctgat putative branch site (score: 4)
ttttactct CT-rich tract
attcaatgtttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatacaggagtagatttgactgtccatataattgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcagAACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCGTGGAGGAACTGGTCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA