RetrogeneDB ID: retro_ogar_1236

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873540.1:7229648..7230545(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000030716
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COPS6
• Ensembl ID: ENSOGAG00000016843
• Aliases: None
• Description: COP9 signalosome subunit 6 [Source:HGNC Symbol;Acc:21749]

Sequence

>retro_ogar_1236
GTCCCCAGCGTGATGGCCTCCCGAGTGACCGGGAGTGTTTTGGTTGCTCTTCCTTCCCTTTTCATTCTCAACATCTCGGA
CCACTGGATCCACATGCGCTCCCAGGAGGGGCGGCCTATGCAAGTGATTGGGGCTCTGATGGGGAAGCAGGAGGGCCGAG
GCATCGAGGTAACGAACTCCTTTGAGCTGCTGTCCCATACTGTGGAAGAAAAGGATTATCTTTGACAAGGAATATTACTA
CACCAAGGAGGAGCAGTTTAGACAGGTATTCGAGGAGCTGCAATTTCTGGGTTACTATACCACAGTGGGGCCCCCGACCC
CTCCGACATCCAGGTGCGTAAGCAGGCGTGAGAGCTAATCGGAGTCCCCTCTCACTTAAGTTGAACCCTTTCACCCAGCA
CACAGATCTTGTCAGCTTTTTGAGTCTGTCGTTGGTATAATAAATGGAGAGGCCACAATGGTATCTGCTGAGCCGGCCTA
CACTCTGGCCACAGGAGAGGCTGAACGCATTGGGGTAGACCGTGTGGCCCAAATGACAGCAACAGGCAGTGGAGAGAATT
CCACTGTGGCCCGACACCGCCTTGCACAACACAGTGCCATGGAGAGGCTGTACAGCTGTATCAAGCTCATTTTGGAGTCC
GTCAAAGCGTCGGAAGCAGGCCAGGTCCCCTTTACCCATGAGATCCTGGGGAGGCCTATGCTCTGTGTCCCTGCCTCCTG
GTGCTCAGCACTGACAAGTTCAAGATGGATTTTTATGATCAATGCAATGAGTGGGGCTCATGGCTTACCTCTGCAATTAT
CACCAAAATGTGCAACATCATGAACCAGTTTGTGAACAAGTTCAATGTCCTCTATGATCGACAAGGCATTGGCAGGCAGA
TGTGGGGGCTCTTTTGG

Alignment

ORF - retro_ogar_1236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 90.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  VPSVMASGVTGSVSVALHPLVILNISDHWIRMRSQEGRPMQVIGALIGKQEGRNIEVMNSFELLSHTVEE
          VPSVMAS.VTGSV.VAL..L.ILNISDHWI.MRSQEGRPMQVIGAL.GKQEGR.IEV.NSFELLSHTVEE
Retrocopy VPSVMASRVTGSVLVALPSLFILNISDHWIHMRSQEGRPMQVIGALMGKQEGRGIEVTNSFELLSHTVEE

Parental  K-IIIDKEYYYTKEEQFKQVFKELEFLGWYTTGGPP-DPSDIHVHKQVCEII-ESPLFLKLNPMTKHTDL
          K.II.DKEYYYTKEEQF.QVF.EL.FLG.YTT.GPP.DPSDI.V.KQ..E.I..SPL.LKLNP.T.HTDL
Retrocopy K>IIFDKEYYYTKEEQFRQVFEELQFLGYYTTVGPP<DPSDIQVRKQA*ELI<RSPLSLKLNPFTQHTDL

Parental  PVS-VFESVIDIINGEATMLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLH
          .VS..FESV..IINGEATM..AE..YTLAT.EAERIGVD.VA.MTATGSGENSTVA.H..AQHSA...L.
Retrocopy -VS<LFESVVGIINGEATMVSAEPAYTLATGEAERIGVDRVAQMTATGSGENSTVARHRLAQHSAMERLY

Parental  SRVKLILEYVKASEAGEVPFNHEIL-REAYALCHCLPVLSTDKFKTDFYDQCND-VGLMAYL-GTITKTC
          S..KLILE.VKASEAG.VPF.HEIL..EAYALC.CL.VLSTDKFK.DFYDQCN..VGLMAYL...ITK.C
Retrocopy SCIKLILESVKASEAGQVPFTHEIL<GEAYALCPCLLVLSTDKFKMDFYDQCNE<VGLMAYL>AIITKMC

Parental  NTMNQFVNKFNVLYDRQGIGRRMRGLFF
          N.MNQFVNKFNVLYDRQGIGR.M.GLF.
Retrocopy NIMNQFVNKFNVLYDRQGIGRQMWGLFW

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_1236 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014814	1 retrocopy	retro_cfam_1389,
Felis catus	ENSFCAG00000003561	1 retrocopy	retro_fcat_522,
Macaca mulatta	ENSMMUG00000013440	1 retrocopy	retro_mmul_387,
Monodelphis domestica	ENSMODG00000004170	1 retrocopy	retro_mdom_220,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Otolemur garnettii	ENSOGAG00000016843	1 retrocopy	retro_ogar_1236 ,
Pteropus vampyrus	ENSPVAG00000005186	1 retrocopy	retro_pvam_690,