Sequence
atgc intronic sequence ATGC exonic sequenceCAACCCGTTCGGGTTCGTGACGGACAACCCGTCGAGCCGCGGCGCCATCCAGCTGCCGGAGTCGCCCGCCCAGGACGGCAATGTCGGCCAGATGCTCTACgtaatgcccacttcgccacacctccttgattccgaactcgtatcattgttgaccatttctagtatgctgtaaagtaatctcgacgcgtgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55180.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55180.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G117531_T02 (Zea mays), 5'ss of exon 1
CAACCCGTTCGGGTTCGTGACGGACAACCCGTCGAGCCGCGGCGCCATCCAGCTGCCGGAGTCGCCCGCCCAGGACGGCAATGTCGGCCAGATGCTCTACgtaatgccc-----acttcgccacacctccttgattccgaactcgtatcattgttgaccatttctagtatgctgtaaagtaatctcgacgcgtgcag-------
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CAATCCGTTCGGGTTCGTGACGGACAACCCCTCCAGCCGCAGCGCCATCCAGCTGCCCGCGGTTCCCGCCGAGGACGGCAATGTCGGCCAGATGCTCTACgtaatgccttatatgcctcgctttgtctacttgacttcttcgtcttctgattacagagcag----ggaaccatatatagaagtcttgtgctctaccaactgagc
upper sequence: LOC_Os04g55180.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G52510.1 (Arabidopsis thaliana), 5'ss of exon 1
CAACCCGTTCGGGTTCGTGACGGACAACCCGTCGAGCCGCGGCGCCATCCAGCTGCCGGAGTCGCCCGCCCAGGACGGCAATGTCGGCCAGATGCTCTACgtaatgcccacttcgccacacctccttgattccgaactcgtatcattgttgaccatttctagtatgctgtaaagtaatctcgac-gcgtgcag--------------------------------------------------------
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TAACCCATTTGGTTTCGTTACAGACAACCCGTCTAGCCGGAGTGCAATTCAGTTACCAGAGTCTCCGGCGGAAGACGGCAATGTCGGCCAAATGCTCTACgtaaatttcacatatttac-tcagttcaattttgaactgtgattgaaattgaaaagat---gcatggttcatatttgcttctattgatttcaaattccattttttatcatagtgttatatttttgttgattgttatgttgtgggtttag
upper sequence: LOC_Os04g55180.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G52510.2 (Arabidopsis thaliana), 5'ss of exon 1
CAACCCGTTCGGGTTCGTGACGGACAACCCGTCGAGCCGCGGCGCCATCCAGCTGCCGGAGTCGCCC-GCCCAGGACGGCAATGTCGGCCAGATGCTCTACgtaatgcccacttcgccacacctcct--tgattccgaactcgtatcattgttgaccatttctagtatgctgtaaagtaatctcgacgcgtgcag
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-------CTCCGGCGGAAGACGGCAATGTCGGCCAAATGCT-CTACGTAAATTTCACATATTTACTCAGTTCAATTTTGAACTGTGATTGAAAT---TGAAAAGATGCATGgttcatatttgcttctattgatttcaaattccattttttatcatagtgttatatttttgttgattgttatgttg-tgggtttag
upper sequence: LOC_Os04g55180.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv09s0002g07500.t01 (Vitis vinifera), 5'ss of exon 1
CAACCCGTTCGGGTTCGTGACGGACAACCCGTCGAGCCGCGGCGCCATCCAGCTGCCGGAGTCGCCCGCCCAGGACGGCAATGTCGGCCAGATGCTCTACgtaatgcccacttcgccacacctccttgattccgaactcgtatcattgttgaccatttctagtatgctgtaaagtaatctcgacgcgtgcag--------------
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CAACCCATTTGGGTTCGTCACCGACAACCCCTCCAGCCGCTCCGCCATTCAGCTTCCCGAGAGTCCCGCCGAGGACGGCAATGTCGGCCAAATGCTCTACgtga-gaccactttac----tttctatgactttgggtggtcttcattgtttttttctgatgtaaattttgtaggttgtcttgtttc-ttcattttttttatgaattMapped 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|29678503|gb|CB674778.1|CB674778EST: AGCTGCCGGAGTCGCCCGCCCAGGACGGCAATGTCGGCCAGATGCTCTAC AGGATCGAGGACAAGGGGAGGGAGTTCGGCTCAAGAGTGAAATCAGGAAAG
genomic: AGCTGCCGGAGTCGCCCGCCCAGGACGGCAATGTCGGCCAGATGCTCTACgtaatgccca ... acgcgtgcagAGGATCGAGGACAAGGGGAGGGAGTTCGGCTCAAGAGTGAAATCAGGAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAACCCGTTCGGGTTCGTGACGGACAACCCGTCGAGCCGCGGCGCCATCCAGCTGCCGGAGTCGCCCGCCCAGGACGGCAATGTCGGCCAGATGCTCTACgtaatgcccacttcgccacacctccttgattccgaactcgtatcattgttgaccatttctagtatgctgtaaagtaatctcgacgcgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG