RetrogeneDB ID: retro_ptro_75

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:21115886..21117410(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000006823
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSPTRG00000019766
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_ptro_75
ATGGAAGAGCCTGCAGCTCCCTCAGAAGCCCACGAGGCAGCCGGGGCCCAGGCAGGTGCTGAGGCAGCAAGGGAGGGTGT
GTCTGGGCCGGACCTTCCCGTCTGTGAGCCCTCCGGGGAATCTGCTGCTCCAGATTCAGCCCTGCCACATGCGGCAAGGG
GCTGGGCCCCCTTCCCTGTAGCTCCAGTCCCTGCCCACCTCCGCAGAGGAGGCCTGAGGCCTGCCCCAGCCTCAGGAGGA
GGAGCCTGGCCCAGTCCGTTGCCGAGCCGAAGCAGCGGCATTTGGACAAAGCAGATCATCTGCAGGTATTATATACATGG
GCAGTGCAAGGAGGGGGAGAACTGTCGCTATTCGCACGACCTTTCTGGTCGGAAGATGGCCACTGAGGGCGGCGTTTTGC
CGCCTGGGGCCTCTGCAGGTGGAGGCCCTAGCACGGCTGCGCACATCGAGCCCCCGACTCAGGAAGTGGCGGAAGCCCCC
CCGGCTGCATCCTCCCTTTCCTTGCCTGTGATTGGCTCGGCTGCTGAAAGGGGTTTCTTTGAAGCGGAGAGAGACAATGC
AGACCGTGGAGCTGCTGGAGGAGCAGGTGTAGAAAGCTGGGCGGATGCCATTGAGTTTGTTCCAGGGCAGCCCTACCGGG
GCCGCTGGGTTGCATCTGCCCCCGAGGCTCCTCTACAGAGCTCAGAGACTGAGAGGAAGCAGATGGCTGTGGGCAGTGGG
TTGCGGTTTTGCTATTATGCTTCCAGGGGAGTTTGCTTTCGTGGGGAGAGCTGTATGTACCTCCATGGAGACATATGCGA
CATGTGTGGGCTGCAGACCTTGCACCCCATGGATGCTGCCCAGAGGGAAGAACATATGAGGGCCTGCATTGAAGCACACG
AGAAAGATATGGAACTCTCGTTTGCTGTGCAGCGTGGTATGGACAAGGTGTGTGGCATCTGCATGGAGGTTGTCTATGAG
AAGGCCAACCCCAATGACCGCCGCTTTGGCATTCTTTCCAATTGCAACCATTCCTTCTGTATTAGGTGTATCCGCAGGTG
GAGAAGTGCCAGACAGTTTGAGAACAGGATCGTCAAGTCTTGCCCACAGTGCAGGGTCACCTCCGAATTGGTCATTCCCA
GTGAGTTCTGGGTGGAGGAGGAGGAAGAGAAGCAGAAACTTATTCAGCAATACAAGGAGGCAATGAGCAACAAGGCCTGC
AGGTATTTTGCGGAAGGCAGGGGTAACTGCCCATTTGGAGACACATGCTTTTACAAGCATGAATACCCTGAGGGCTGGGG
AGATGAGCCTCCTGGGCCAGGTGGTGGGTCATTCAGCGCATACTGGCATCAACTTGTGGAGCCTGTGCGAATGGGAGAGG
GCAACATGCTCTATAAAAGCATTAAGAAGGAGCTTGTCGTGCTTCAGCTGGCCAGTCTGTTGTTTAAGCGGTTTCTTTCA
CTGAGAGATGAGTTACCCTTCTCTGAGGACCAGTGGGACTTGCTTCATTATGAGCTGGAAGAATATTTCAATTTGATTCT
GTAG

Alignment

ORF - retro_ptro_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.8 %
• Parental protein coverage: 60.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TELTTKSSLAASSSLSSIVGPLVEMNTGEAESRNSNF-ATVGAGSEDWVNAIEFVPGQPYCGRTAPSCTE
          T........AASS......G...E....EAE..N....A..GAG.E.W..AIEFVPGQPY.GR...S..E
Retrocopy TQEVAEAPPAASSLSLPVIGSAAERGFFEAERDNADRGAAGGAGVESWADAIEFVPGQPYRGRWVASAPE

Parental  APLQGSVTKEESEKEQTAVETKKQLCPYAAVGECRYGENCVYIHGDSCDMCGLQVLHPMDAAQRSQHIKS
          APLQ.S....E.E..Q.AV......C.YA..G.C..GE.C.Y.HGD.CDMCGLQ.LHPMDAAQR..H...
Retrocopy APLQSS----ETERKQMAVGSGLRFCYYASRGVCFRGESCMYLHGDICDMCGLQTLHPMDAAQREEHMRA

Parental  CIEAHEKDMELSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKII
          CIEAHEKDMELSFAVQR..D.VCGICMEVVYEKANP..RRFGILSNCNH..C..CIR.WRSA.QFE..I.
Retrocopy CIEAHEKDMELSFAVQRGMDKVCGICMEVVYEKANPNDRRFGILSNCNHSFCIRCIRRWRSARQFENRIV

Parental  KSCPECRITSNFVIPSEYWVEEKEEKQKLILKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAYPDGRRE
          KSCP.CR.TS..VIPSE.WVEE.EEKQKLI..YKEAMSNKACRYF.EGRG.CPFG..CFYKH.YP.G...
Retrocopy KSCPQCRVTSELVIPSEFWVEEEEEKQKLIQQYKEAMSNKACRYFAEGRGNCPFGDTCFYKHEYPEGWGD

Parental  EPQRQKVGTSSRY
          EP.....G..S.Y
Retrocopy EPPGPGGGSFSAY

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	2.32 RPM	62.44 RPM
SRP007412_cerebellum	0.68 RPM	123.61 RPM
SRP007412_heart	0.03 RPM	87.53 RPM
SRP007412_kidney	0.00 RPM	90.01 RPM
SRP007412_liver	0.03 RPM	52.73 RPM
SRP007412_testis	4.43 RPM	1105.68 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_75 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_75 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_75 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 47 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	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,