RetrogeneDB ID: retro_pabe_3435

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:92706070..92706965(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSPPYG00000018057
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_pabe_3435
CCTTCCTGCACTGAAGCACCTCTGCAGGACTCAGTGACCAAGGAAGAATCAGAGAAAGAGAAAAACTGCTGTGGAAACCA
AGAAGCAGCTGTGCCCCTGTGCTGCAGTGAGAGAGTGCCAAGATGGGGAGAACTGTGTGCCTCTCCACGGAGATTCATGT
GACATGTGTGGACTGCAGGTCCTGCATCCCATGGCTGCTGCCCAGAGATCACAGCGTATAAAATTGTGCATTGAGGCCCA
TGAGAAGGACATGGAGCTCTCACTTGCTGTGCAGCACAGCAAGGACGTGGTGTATGGGATCTGCATGGAGGTGGTCTATG
AGAAAGCAAACCCCAGCAAGTGCCTCTTCAGGATCCTCTCCAACTGCAACCACGCCTACTGTCTCAAGTGCATTCGCAAA
TGGAAGAGTGCTAAGCAATTTCAGAGCAAGATTATAAAGTCCTGCCCAGATTGCCAGATCACATCTAACTTTGTCATTCC
AAGTGAGTCCTGGGTGGAAGAGAAAGAAGAGAAGCAGAAACTCATTCAGAAATACAAGGAGGCGTTGAGCAACAAGGCTT
GCAGGTATTTTGATGAAGGACGTGGGAGCTGCCCATTTGGAAGGAATTGTTTTTACAAGCATGCGTACCCTGATGGCCTT
ACAGAGGAGCCGTAGAGGCAGAAAGTGGGAACATCAAGCAGAAACTGGGTCCAATGAAGGAACCACTTCTGAGAACTCAT
TGAAGAAAGAGATAGCAGCAACCCTTTTGACAATGATGAAGAGGTTGTCACCTTTGAGCTGGGCGAGATGTTGCTTATGC
TTTTGGCTGCAGGTGGGGATGACGAACTGGCAGACTCTGAAGATGAGTGGGACTTGTTTCATGATGAGCTGGAAGATTTT
TATGATTTGGATCTA

Alignment

ORF - retro_pabe_3435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.33 %
• Parental protein coverage: 71.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSCTEAPPQGSVTKEESEKEQ-TAVETKKQLCPYAAVGECRYGENCVYLHGDSCDMCGLQVLHPMDAAQR
          PSCTEAP.Q.SVTKEESEKE..TAVETKKQLCP.AAV.EC..GENCV.LHGDSCDMCGLQVLHPM.AAQR
Retrocopy PSCTEAPLQDSVTKEESEKEK>TAVETKKQLCPCAAVRECQDGENCVPLHGDSCDMCGLQVLHPMAAAQR

Parental  SQHIKSCIEAHEKDMELSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQ
          SQ.IK.CIEAHEKDMELS.AVQ.SKD.V.GICMEVVYEKANPS...F.ILSNCNH.YCLKCIRKW.SAKQ
Retrocopy SQRIKLCIEAHEKDMELSLAVQHSKDVVYGICMEVVYEKANPSKCLFRILSNCNHAYCLKCIRKWKSAKQ

Parental  FESKIIKSCPECRITSNFVIPSEYWVEEKEEKQKLILKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAY
          F.SKIIKSCP.C.ITSNFVIPSE.WVEEKEEKQKLI.KYKEA.SNKACRYFDEGRGSCPFG.NCFYKHAY
Retrocopy FQSKIIKSCPDCQITSNFVIPSESWVEEKEEKQKLIQKYKEALSNKACRYFDEGRGSCPFGRNCFYKHAY

Parental  PDGRREEPQRQKVGTSSRYRAQRRNHFWELIEERENSNPFDNDEEEVVTFELGEMLLMLLAAGGDDELTD
          PDG..EEP.RQKVGTSSR...Q.RNHF.ELIEER..SNPFDND.EEVVTFELGEMLLMLLAAGGDDEL.D
Retrocopy PDGLTEEP*RQKVGTSSRNWVQ*RNHF*ELIEERDSSNPFDND-EEVVTFELGEMLLMLLAAGGDDELAD

Parental  SEDEWDLFHDELEDFYDLDL
          SEDEWDLFHDELEDFYDLDL
Retrocopy SEDEWDLFHDELEDFYDLDL

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	90.12 RPM
SRP007412_cerebellum	0.49 RPM	95.21 RPM
SRP007412_heart	0.06 RPM	43.38 RPM
SRP007412_kidney	0.10 RPM	62.02 RPM
SRP007412_liver	0.03 RPM	35.47 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3435 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3435 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3435 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4197
Pan troglodytes	retro_ptro_2849
Gorilla gorilla	retro_ggor_2813

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 53 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,
Erinaceus europaeus	ENSEEUG00000001133	1 retrocopy	retro_eeur_643,
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,
Macropus eugenii	ENSMEUG00000007399	1 retrocopy	retro_meug_1659,
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	ENSOGAG00000009877	2 retrocopies	retro_ogar_3468, retro_ogar_424,
Ochotona princeps	ENSOPRG00000010353	1 retrocopy	retro_opri_1073,
Procavia capensis	ENSPCAG00000014683	1 retrocopy	retro_pcap_19,
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,
Tupaia belangeri	ENSTBEG00000004564	2 retrocopies	retro_tbel_1410, retro_tbel_71,
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,