RetrogeneDB ID: retro_ogar_3304

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873771.1:1438649..1440062(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000031706
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000007206
• Aliases: None
• Description: None

Sequence

>retro_ogar_3304
ATGTCGGACTTCGAAGAGTTCGAGCGGCAGCTTAATGAGAATAAACAAGAGCGGGACAAAGAGAACCGCCACAGGAAGCG
CAGCCACAGCCGCCCTCGAAGCCGGGACCGCAAGCGTCGGAGCCGGAGCCGGCACCGGCGCAACCGGGACCAGCGGAGCG
CCTCCCGGGACAGGCGGCGGCGAAGCAAACCTTTGACCAGAGGCGCTAAAGAGGAGCACGGTGGGTTGATTCGTTCCCCC
CGCCATGAGAAGAAGAAAAAGGTCCGTAAATACTGGGACGTGCCCCCCCCTGGCTTTGAGCACATCACTCCAATGCAGTA
CAAGGCCATGCAAGCTGCAGGTCAGATTCCAGCCACTGCCCTTCTCCCCACCATGACCCCTGATGGGCTTGCTGTGACCC
CGACGCCCGTGCCTGTGGTGGGGAGCCAGATGACCAGACAGGCCCGTCGCCTGTATGTGGGCAATATCCCCTTTGGCATC
ACTGAGGAGACCATGATGGAGTTCTTCAACACCCAGATGCGCCTGGGGGGGCTGACCCAAGCCCTTGGCAACCCTGTCTT
GGCTGTGCAGATTAACCAAGACAAGAATTTTGCCTTTTTGGAGTTCCGTTCAGTGGATGAGACTACCCAGGCCATGGCCT
TCGATGGCATCATCTTCCAAGGCCAGTCACTGAAGATCCGCCGGCCTCATGACTACCAGCCGCTGCCTGGCATGTCAGAG
AATCCCTCTGTCTATGTTCCTGGAGTTGTGTCCACTGTGGTCCCTGACTCTGCCCACAAGCTGTTCATTGGGGGCTTACC
CAATTATCTGAATGATGACCAGGTGAAAGAACTGCTGACATCGTTTGGGCCTCTTAAGGCCTTCAACCTGGTCAAGGACA
GTGCCACCGGGCTCTCCAAGGGCTACTCCTTCTGTGAGTACGTGGACATCAATGTCACAGATCAGGCCATCGCAGGGCTG
AATGGGATGCAGCTGGGGGATAAGAAGCTGCTTGTCCAGAGGGCAAGTGTGGGAGCCAAGAATGCCACGCTGAGCACCAT
CAATCAGACGCCTGTGACCCTACAAGTGCCGGGCCTGATGAGCTCCCAGGTACAGATGGGTGGCCACCCCACCGAGGTCC
TGTGCCTCATGAATATGGTGCTGCCCGAGGAGCTGCTGGATGATGAAGAGTATGAGGAGATTGTGGAAGATGTGCGAGAT
GAGTGCAGCAAGTATGGGCTCGTCAAGTCTATCGAGATCCCCCGGCCTGTGGATGGTGTCGAGGTGCCTGGCTGCGGAAA
GATCTTTGTGGAGTTCACCTCTGTGTTTGACTGCCAGAAAGCCATGCAGGGCCTGACAGGCCGCAAGTTTGCCAACAGAG
TGGTTGTCACAAAGTATTGTGACCCCGACTCTTACCACCGCCGGGATTTCTGG

Alignment

ORF - retro_ogar_3304 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.84 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDFDEFERQLNENKQERDKENRHRKRSHSRSRSRDRKRRSRSRDRRNRDQRSASRDRRRRSKPLTRGAK
          MSDF.EFERQLNENKQERDKENRHRKRSHSR.RSRDRKRRSRSR.RRNRDQRSASRDRRRRSKPLTRGAK
Retrocopy MSDFEEFERQLNENKQERDKENRHRKRSHSRPRSRDRKRRSRSRHRRNRDQRSASRDRRRRSKPLTRGAK

Parental  EEHGGLIRSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVPVV
          EEHGGLIRSPRHEKKKKVRKYWDV...GFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVPVV
Retrocopy EEHGGLIRSPRHEKKKKVRKYWDVXXXGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVPVV

Parental  GSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ
          GSQMTRQARRLYVGNIPFGITEE.MM.FFN.QMRLGGLTQA.GNPVLAVQINQDKNFAFLEFRSVDETTQ
Retrocopy GSQMTRQARRLYVGNIPFGITEETMMEFFNTQMRLGGLTQALGNPVLAVQINQDKNFAFLEFRSVDETTQ

Parental  AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLT
          AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLT
Retrocopy AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLT

Parental  SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATLVSPPST
          SFGPLKAFNLVKDSATGLSKGY.FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATL....ST
Retrocopy SFGPLKAFNLVKDSATGLSKGYSFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATL----ST

Parental  INQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRP
          INQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRP
Retrocopy INQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRP

Parental  VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW
          VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW
Retrocopy VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3304 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000018056	1 retrocopy	retro_lafr_94,
Myotis lucifugus	ENSMLUG00000011051	2 retrocopies	retro_mluc_406, retro_mluc_797,
Macaca mulatta	ENSMMUG00000004810	1 retrocopy	retro_mmul_30,
Mus musculus	ENSMUSG00000030435	3 retrocopies	retro_mmus_2251, retro_mmus_3663, retro_mmus_991,
Otolemur garnettii	ENSOGAG00000007206	1 retrocopy	retro_ogar_3304 ,