RetrogeneDB ID: retro_ogar_1033

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873534.1:18355564..18355918(+)
• Located in intron of: ENSOGAG00000012090

Retrocopy information

• Ensembl ID: ENSOGAG00000024937
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC4
• Ensembl ID: ENSOGAG00000026074
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 4, 20kDa [Source:HGNC Symbol;Acc:707]

Sequence

>retro_ogar_1033
CAAGAACTCCTGTTACAACCTGTGACCATCAGCAGAAATGAAAAGGAAAAGGTTCTGATTGCTGTCCCAGTCAGCATCGC
TGTGAAACAGGCTGATGAGATTGAGATTTTATGCCACGAGTTTATGCGCTTCATGATGATGCGAGCAGAGAACTTTTTTA
TCCTTCGAAGGAAACCAGTGGAGGGGTATGACATTAGTTTTCTGATCACCAACTTCCACACACAGCAAATGTACAAACAC
AGGTTGGTGGACGTTGTGATCCACTTCACGGAGGGGATTGACAAGGAGATGAGTGAGGTGACACTGTCAGTCAATGCCCG
TGCACACACTGTGGCTGAGGAGTTCCTCAAGAAC

Alignment

ORF - retro_ogar_1033 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.81 %
• Parental protein coverage: 96.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KELLLQPVTISRNEKEKVLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYD
          .ELLLQP........EK...E.....V.VSIAVKQADEIE.ILCH.FMRFMMMRAENFFILRRKPVEGYD
Retrocopy QELLLQP--VTISRNEK---EKVLIAVPVSIAVKQADEIE-ILCHEFMRFMMMRAENFFILRRKPVEGYD

Parental  ISFLITNFHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKN
          ISFLITNFHT.QMYKH.LVD.VIHF.E.IDKE.SE..LSVNARA..VAEEFLKN
Retrocopy ISFLITNFHTQQMYKHRLVDVVIHFTEGIDKEMSEVTLSVNARAHTVAEEFLKN

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_1033 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007964	2 retrocopies	retro_btau_680, retro_btau_849,
Callithrix jacchus	ENSCJAG00000016175	1 retrocopy	retro_cjac_1681,
Myotis lucifugus	ENSMLUG00000025088	1 retrocopy	retro_mluc_2078,
Monodelphis domestica	ENSMODG00000005136	1 retrocopy	retro_mdom_1390,
Otolemur garnettii	ENSOGAG00000026074	2 retrocopies	retro_ogar_1033 , retro_ogar_875,