Sequence
atgc intronic sequence ATGC exonic sequencegtaagagttctgaacagtgcctttggcccctgtctattgcttaatacttcagaacctgatttgcaagttcaccactactagATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g28060.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g28060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G319760_T01 (Zea mays), 3'ss of exon 6
gtaagagttctgaacagtgcctttggcccctg--tctattgcttaatacttcagaacctgatttgcaagttcaccactactagATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAG
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gtaatgattcttgaaaatgctttgtgctgcttgttccattgctatatattgcactcactgacttggatactcacatataatagATGGAAATGGCTTCAAAACTAGCACGATGAGGCTTGGGGCAGATGCTATTGTATTCACATGCACTAAAGATGATAG
upper sequence: LOC_Os06g28060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G19100.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------------------------gtaagagttctgaacagtgcctttggcccctgtctattgcttaatacttcagaacctgatttgcaagttcaccactactagATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGC-ACACAAGATAATAG
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gtatgaatctttcgcttcattctctaaactctttatctttagttatgattctgcaacacatatctctgattctcattttgcattacataccattagttatgattttgaaactcagatctttaattatgattctgcatctcaccttca---ttattatctttagATGGAAATGGTTTCAAGACCAGCACAATGAGACTTGGGGCAGATGTCATCGTCTTCAGCCGCCATTCGAAGAACCA-
upper sequence: LOC_Os06g28060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv17s0000g08750.t01 (Vitis vinifera), 3'ss of exon 5
gtaagagttctgaacagtgcctttggcccctgtctattgcttaatacttcagaacctgatttgcaagttcaccactactagATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAG
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gtaaggatgttatgtttttcattctgcattttttttctcctt----ccatatgagttggctgatgtgt--agcattac-agATGGAAATGGCTTCAAGACCAGCTCTATGAGACTTGGAGCAGATGTTATTGTCTTCAGCCGCCACCTGGACAATGG
upper sequence: LOC_Os06g28060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv14s0066g00870.t01 (Vitis vinifera), 3'ss of exon 6
gtaagagttctgaacagtgcctttggcccctgtctattgcttaatacttcagaacctgatttgcaagttcaccactactagATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAG
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gtatggattcc--acctctcttctaccatttacatttttcctcatcatcttgtactaagtggttggcttctatcctttcagATGGAAATGGGTTCAAGACAAGCACAATGAGACTTGGAGCGGATGTGATTGTATTCAGCCGCCACTTGAAAGAGAGMapped 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|29636270|gb|CB641279.1|CB641279EST: CATGAGCTTTGGGTTCTCCNNNNNNNGTGGGAATTCATCCATTGGACAAT ATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTG
genomic: CATGAGCTTTGGGTTCTCCAAAAAAAGTGGGAATTCATCCATTGGACAATgtaagagttc ... ccactactagATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccctgtctattgcttaatacttcagaacctgatttgcaagttcaccactactagATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAG
acctgat putative branch site (score: 4)
ttaatactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagttctgaacagtgcctttggcccctgtctattgcttaatacttcagaacctgatttgcaagttcaccactactagATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC