Sequence
atgc intronic sequence ATGC exonic sequence...tttttctgtatttcaagcttgaatgcttgattactctgctatctgttctctagtatgtatttcagtctattgcccttaaactgttatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g44922.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 9
tttttctgtatttcaagcttgaatgcttgatt--actctgctatctgttctctagtatgtatttcagtc-tattgcccttaaactgttatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG
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--agttcacatagcacatttctattctcgattcagagcaaagaaccttctttttttgtttgcttcagccatcttgactttaccagcttatctac-tattgtagGGTTCATTGCGATGTATGCTACTCTTGCTAGTCGAGATGTG
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 9
------tttttctgtatttcaa--gcttgaatgcttgattactctgctatctgttctctagt-atgtatt---tcagtctattgcccttaaactgttat-------attcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG-----------------------------------------------------------
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gtaagtttcttgaatgcctccactgatcagattaatcattagcatcctgtacttcaaccaatgacatattatgttaataaattattttctcgatgtaattatatggatgcatggtgcagGGTTTATTGCAATGTATGCTACTCTGGCCAGTAGGGATGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTCACCTTGAAGGTCCAGGTGGACTTTTTGA
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 9
-----tttttctgtatttcaagcttgaatgcttgattactctgctatctgttctctagtatgtatttcagtctat-tgcccttaaactgttatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG-----------------------------------------------------------
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agaaaagaattgctgttataagttcaaaagtt--attccattga-agctgttagcgaa-attgattttgcttcatatatgcttta--ttttggacttatgatacagGATTTATTGCAATGTATGCTACTCTTGCGAGTCGAGACGTGGATTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTCCTGGTGGACTCTATGA
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
tttttctgtatttcaagcttgaatgcttgattactctgctatctgttctctagtatgtatttcagtctattgcccttaaactgt----tatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG-----------------------------------------------------------
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--gaaaagaacggctagtatga-tattcaaaagttcttccattgacattgtcat-caaacttgactttgcttcatatatgctttattttggatttatgatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 9
----tttttctgtatttcaagcttgaatgcttgattactctgctatctgttctctagt-atgtatttcagtctattgcccttaaactgttatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG-----------------------------------------------------------
||| || || | ||| | | | | || |||| || | | | |||| || ||| | | | ||| ||||||||| |||||||||||||||||||| || ||| | ||||||
gtaagtttcttgaatgcctccactgatcagattaatcattagcatcctgtacttcattgacatattat-gttaattattttcttgatacatggtgcatggtgcagGGTTTATTGCAATGTATGCTACTCTGGCCAGTAGGGATGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTCACCTTGAGGGTCCAGGTGGACTTTTTGA
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------------tttttctgtatttcaagcttgaatgcttgattactctgctatctgttctctagtatgtatttcagtctattgcccttaaactgttatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG-----------------------------------------------------------
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gtaagttcacagaagaatctaggagagcagtaatgcatac--aaatattagaccacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA
upper sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------------------------tttttctgtatttcaagc--------ttgaatgcttga--ttactctgctatctgttctctagta---tgtatttcagtctattgcccttaaactgttatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG-----------------------------------------------------------
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gtaacttttacatttatatttgatattcagatttacttaaaagtttttaactgtgtaagtgaagtgaggaacgttgaattattggatttgttgtgcaagcctcttccaagtaatcttgatttccaatttttcctacaaagtatttggatttgatgtgcagGATTCATTGCGATGTATGCTACACTTGCCAGTCGAGATGTAGACTGTTGTTTGATTCCAGAGTCACCATTCTATCTTGAAGGGAAAGGTGGACTTTTTGAMapped 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|27576264|gb|CA998958.1|CA998958EST: CAGTGCTGAGAATGGAATAGGCTTAGTAAAACTGATGGGCCGTTATAGTG GGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTGGACTGCTGC
genomic: CAGTGCTGAGAATGGAATAGGCTTAGTAAAACTGATGGGCCGTTATAGTGgtacgtattt ... catcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTGGACTGCTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctagtatgtatttcagtctattgcccttaaactgttatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG
ttcatctt CT-rich tract
ttaaactgttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttctgtatttcaagcttgaatgcttgattactctgctatctgttctctagtatgtatttcagtctattgcccttaaactgttatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- -ttctgta
- - - - - - - - - -tgaatgc
- - - - - - - - - - - - - - - - -ctctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccctt