RetrogeneDB ID: retro_ogar_1054

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873534.1:18343984..18344819(-)
• Located in intron of: ENSOGAG00000012090

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: AP1AR
• Ensembl ID: ENSOGAG00000001631
• Aliases: None
• Description: adaptor-related protein complex 1 associated regulatory protein [Source:HGNC Symbol;Acc:28808]

Sequence

>retro_ogar_1054
ATGGGGACCTGCTGCTGGACACAGTGCTTTGGGCTGCTTTGCAAGGAAGCCGGGAAGCTGCAACGTGCAGGAGGCGGCGG
AGGATCCAAGTATTTTAGAACATGCTGAAGAGGTGAGCACTAACTATAGAGTTTGAGAGCCTAGTAGAAAGTGATGAAGG
GGAGAGCCCAGGAAGCAGTCATAGGCCTCTTACTGAGAAAGAAATTATTGACCTAAGAGAGAGACATTATGATTCTATTG
CTGAAAAACAGAAAGATCTTGATAAGAGAATTCAAAATGAGTTAGCCTTACAAGAAGAGAAGTTAAGACTAGAAGAAGGA
GCTTTACACGCTGCACAGCGTGAAGCAGCCAGGGCAGCAAAGCCGCGAAAGCTCTTGGAGCAAGAGAGGCAGAGAATTGT
GCAACGATCTCTCATCCTTCTCACAACAATGGAGAATATCAAAGTTCAGGACCAGAAGATGACTTTGAATCTTGTTTGAG
AAATGGAAAGTCACAGTATGAAGTTTTTCGAAGTAGTAGACTGCCATCAGATGCCACAGTTTTGACACCAAATACAGAAA
GCAGTTGTGATTTAATGACCAAAACTAAATCAACTAGTGGAAATGACGACAGCACATCCCTAGATCCCGACCGGGAAGAT
GAAGAAGGTATGAATAGAATGCTTCCAATGAGAGAAAGGTCCAAAACAGAGGAAGCCGGTCTCCGGGCGGTGCTTAAGTA
CAGCAGCAAGTCTGGGAGTGATCCTACCTCAGCCTCTGACGATTCCAACCAGCTGGAATGGGAGAATGACTTTGTTAGTG
CCAAAATGGATGATAACAGCAATTCCGAGTATTCT

Alignment

ORF - retro_ogar_1054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.46 %
• Parental protein coverage: 92.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGNCCWTQCFGLLRKEAGRLQRVGGGGGSKYFRTCSRGEH-LTIEFENLVESDEGESPGSSHRPLTEEEI
          MG.CCWTQCFGLL.KEAG.LQR.GGGGGSKYFRTC.RGEH.LTIEFE.LVESDEGESPGSSHRPLTE.EI
Retrocopy MGTCCWTQCFGLLCKEAGKLQRAGGGGGSKYFRTC*RGEH<LTIEFESLVESDEGESPGSSHRPLTEKEI

Parental  IDLRERHYDSIAEKQKDLDKKIQNELALQEEKLRLEEEALYAAQREAARAA-KQRKLL-EQERQRIMQRY
          IDLRERHYDSIAEKQKDLDK.IQNELALQEEKLRLEE.AL.AAQREAARAA.K..K.L...E........
Retrocopy IDLRERHYDSIAEKQKDLDKRIQNELALQEEKLRLEEGALHAAQREAARAA<KAAKALGAREAENCATIS

Parental  HPS-NNGEYQSSGPEDDFESCLRNVKSQYEVFRSSRLSSDATVLTPNTESSCDLMTKTKSTSGNDDSTSL
          HPS.NNGEYQSSGPEDDFESCLRN.KSQYEVFRSSRL.SDATVLTPNTESSCDLMTKTKSTSGNDDSTSL
Retrocopy HPSHNNGEYQSSGPEDDFESCLRNGKSQYEVFRSSRLPSDATVLTPNTESSCDLMTKTKSTSGNDDSTSL

Parental  DLEWEDEEGMNRMLPMRERSKTEEDILRAALKYSSKKTGSNPTSASDDSNGLEWENDFVSAEMDDNGNSE
          D...EDEEGMNRMLPMRERSKTEE..LRA.LKYSS.K.GS.PTSASDDSN.LEWENDFVSA.MDDN.NSE
Retrocopy DPDREDEEGMNRMLPMRERSKTEEAGLRAVLKYSS-KSGSDPTSASDDSNQLEWENDFVSAKMDDNSNSE

Parental  YS
          YS
Retrocopy YS

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_1054 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007262	2 retrocopies	retro_chof_1995, retro_chof_8,
Monodelphis domestica	ENSMODG00000005746	1 retrocopy	retro_mdom_160,
Oryctolagus cuniculus	ENSOCUG00000004413	1 retrocopy	retro_ocun_91,
Otolemur garnettii	ENSOGAG00000001631	1 retrocopy	retro_ogar_1054 ,
Sus scrofa	ENSSSCG00000009128	1 retrocopy	retro_sscr_245,