RetrogeneDB ID: retro_ogar_3468

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873869.1:50270..51474(+)
• Located in intron of: ENSOGAG00000001109

Retrocopy information

• Ensembl ID: ENSOGAG00000034748
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSOGAG00000009877
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_ogar_3468
GACAGTCCATATGGTGTAGTGTGCAAGTATTATCATCGAAGGTACTGTATTTATGGAGACTGCTACAGATAGGAACATAG
CAAGCCATTGAAACAGGAAGAAGCAACTGCTACAGACCTAACTGCAAAGTCATCTGTTCCTGCTTCCTCAAGTCTATCTT
TAGCAGTCAGACCTCTTGTTGAAATGAACACCGGTGAAGCTGAGTCAAGAAATCCAAACTTTAGAAGTGTAGGAGCAGGT
CCAGAGGACTGGGTGAATGCTACTGAGTTTGCTCCTGGACAACCCTGCTGTGTCCGTACTGCGCCTTCCTGCACTGAAGC
ACCCCTGGCAGGGCTCAGTAACCAAGGAAGAATCAGAGAAAGAGCAAATCACCATGGAAGCAAAGAAACAGCTTTGCCCC
TGTGCTGGCGTGAGGGAGTGCCGATATAGGGAAAACTGTGTATCTCCACGGGGACTCATGTGATACATGTGGGCTGCAGG
TCCTACATCCAATGGATGCTGCCCAGAGATCACAACAGATAAAATCTTGCATTGAGGTGCAAGAGAAGGACATGGAGCTC
TCGTTTGCTGTGCAGCACAGCAAGGAAATGGTGTGTGGGATCTGCATGGAGGTGGAGTATGAGAAAGCCAACCCCAGTGA
GCGCTGCTTTGCGATCCTCTATAACTGCAACCACACCTACCATCTCAAGTGCATTTACAAGTGGAGGAGTGCTAAGCAAT
TTGGGAGCAAGATCATAAAGTCCTGCCCAGAATGCTGGATCACATCTAACTTTGTTATTCCAAGTGAGTACTGGGTGGAG
GAGAAAGAAGAGTAGCAGAAACTCATTCAGAAATACAAGGAGGCAATGAGCAACAAGTCGTGCAGGTATTTGATGAAGGA
CGTGGGATCTGCCCATTTGGAGGGAACTGCTTTTACAGGCATCTGTACCCTGATGGACATAGAGAGGAGCCACAGAGACA
GAAAGTGGGAACATCAAGCAGATACCGGGCCCAATGAAGGAACCACTTCTGGGAGCTCATTGAGGAAAGAGAGAACAGCA
GTCAACGATGCTTTGACAATGATGAAGAAGAGGTTGTCACTTTTGAGCTGGGTGAGATGTTGCTTATGCTTTTGGCTGCA
GGTAGGGATGATGAACTGACAGACTCTGAAGATGAGTGGGACTTGTTTCATGATGAGCTGGAAGATTTTTATGAGTTGGA
TCTA

Alignment

ORF - retro_ogar_3468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.17 %
• Parental protein coverage: 81.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DSPYGVVCKYYQRGYCIYGDRCRYEHSKPLKQEEATATDLTTKSSVAASSSLSSAVGPLVEMNTSEAESR
          DSPYGVVCKYY.R.YCIYGD..R.EHSKPLKQEEATATDLT.KSSV.ASSSLS.AV.PLVEMNT.EAESR
Retrocopy DSPYGVVCKYYHRRYCIYGDCYR*EHSKPLKQEEATATDLTAKSSVPASSSLSLAVRPLVEMNTGEAESR

Parental  NSNFRSVGAGPEDWVNAIEFVPGQPYCGRTAPSCTEAPL-QGSVTKEESEKEQNTVETKKQLCPYAAV-G
          N.NFRSVGAGPEDWVNA.EF.PGQP.C.RTAPSCTEAPL.QGSVTKEESEKEQ.T.E.KKQLCP.A.V.G
Retrocopy NPNFRSVGAGPEDWVNATEFAPGQPCCVRTAPSCTEAPL>QGSVTKEESEKEQITMEAKKQLCPCAGV>G

Parental  ECRYGENCVYLHGDSCDMCGLQVLHPMDAAQRSQHIKSCIEAHEKDMELSFAVQRSKDMVCGICMEVVYE
          ....G...VYLHGDSCD.CGLQVLHPMDAAQRSQ.IKSCIE..EKDMELSFAVQ.SK.MVCGICMEV.YE
Retrocopy SADIGKT-VYLHGDSCDTCGLQVLHPMDAAQRSQQIKSCIEVQEKDMELSFAVQHSKEMVCGICMEVEYE

Parental  KANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPSEYWVEEKEEKQKLIQK
          KANPSER.F.IL.NCNHTY.LKCI.KWRSAKQF.SKIIKSCPEC.ITSNFVIPSEYWVEEKEE.QKLIQK
Retrocopy KANPSERCFAILYNCNHTYHLKCIYKWRSAKQFGSKIIKSCPECWITSNFVIPSEYWVEEKEE*QKLIQK

Parental  YKEAMSNKACRY-FDEGRGSCPFGGNCFYKHAYPDGRREEPQRQKVGTSSRYRAQRRNHFWELIEERENS
          YKEAMSNK.CRY.FDEGRG.CPFGGNCFY.H.YPDG.REEPQRQKVGTSSRYRAQ.RNHFWELIEERENS
Retrocopy YKEAMSNKSCRY<FDEGRGICPFGGNCFYRHLYPDGHREEPQRQKVGTSSRYRAQ*RNHFWELIEERENS

Parental  SP--FDNDEEEVVTFELGEMLLMLLAAGGDDELTDSEDEWDLFHDELEDFYDLDL
          S...FDNDEEEVVTFELGEMLLMLLAAG.DDELTDSEDEWDLFHDELEDFY.LDL
Retrocopy SQRCFDNDEEEVVTFELGEMLLMLLAAGRDDELTDSEDEWDLFHDELEDFYELDL

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_3468 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 20 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni	ENSCHOG00000011015	3 retrocopies	retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Dasypus novemcinctus	ENSDNOG00000019564	2 retrocopies	retro_dnov_1011, retro_dnov_388,
Felis catus	ENSFCAG00000024942	1 retrocopy	retro_fcat_67,
Homo sapiens	ENSG00000133606	4 retrocopies	retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Microcebus murinus	ENSMICG00000002114	1 retrocopy	retro_mmur_1184,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus	ENSMUSG00000029922	1 retrocopy	retro_mmus_2663,
Nomascus leucogenys	ENSNLEG00000001921	4 retrocopies	retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii	ENSOGAG00000003255	1 retrocopy	retro_ogar_3196,
Otolemur garnettii	ENSOGAG00000009877	2 retrocopies	retro_ogar_3468 , retro_ogar_424,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes	ENSPTRG00000019766	5 retrocopies	retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa	ENSSSCG00000016498	2 retrocopies	retro_sscr_43, retro_sscr_637,
Tarsius syrichta	ENSTSYG00000009996	3 retrocopies	retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus	ENSTTRG00000009528	2 retrocopies	retro_ttru_1064, retro_ttru_1128,