RetrogeneDB ID: retro_ptro_602

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:40139984..40140435(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC9
• Ensembl ID: ENSPTRG00000017047
• Aliases: None
• Description: None

Sequence

>retro_ptro_602
CAAGCAGCAAAGAGAAAGACAATGGTATGTTTCCATTGCAGAAAACCTGGTCATACAACTGCAGATTGCCCAGTTGCCCT
AGAAAATCAAGATACGGGCACTGCAACGTGTTCTGAGTCTGGGTCCATGGAGCGCAAAATGATCAAGCGCCGGGCTAAAG
TAGCCCTGGCTCTTAATTAATTTCCTTTTGCGAAATATTTGTTTGTAGGAAATGAGACAGCTGTCCAGATCTTGTCCTGA
TCATCCCAAAGGACTCTGTGCTGATGGTGGTGGTTGCCAACTTTGTTGCTCTATGGAATATTTTAAGAAGGATTGTCCTG
AAAGTCAGAATTCAGATTTTGGAATGGTCACGGTTGATTGCTGGTCAAAGGGAGTGAGTGCAGACTCTGAAGAAATTGGA
TGACTTAAATTACAGAAATCCAAAACAAAGATACCTAAAATTGTTATTTTT

Alignment

ORF - retro_ptro_602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.23 %
• Parental protein coverage: 55.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAAKKNAMVCFHCRKPGHGIADCPAALENQDMGTGICYRCGSTEHEITKCKAKVDPALGEFPFAK-CFVC
          QAAK...MVCFHCRKPGH..ADCP.ALENQD.GT..C...GS.E....K..AKV..AL..FPFAK..FVC
Retrocopy QAAKRKTMVCFHCRKPGHTTADCPVALENQDTGTATCSESGSMERKMIKRRAKVALALN*FPFAK<IFVC

Parental  G-EMGHLSRSCPDNPKGLYADGGGCKLCGSVEHLKKDCPESQNSE-RMVTVGRWAKGMSADYEEILDVPK
          ..EM..LSRSCPD.PKGL.ADGGGC.LC.S.E..KKDCPESQNS...MVTV..W.KG.SAD.EEI....K
Retrocopy R<EMRQLSRSCPDHPKGLCADGGGCQLCCSMEYFKKDCPESQNSDFGMVTVDCWSKGVSADSEEIG*L-K

Parental  PQKPKTKIPKVVNF
          .QK.KTKIPK.V.F
Retrocopy LQKSKTKIPKIVIF

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	4.45 RPM
SRP007412_cerebellum	0.04 RPM	9.68 RPM
SRP007412_heart	0.00 RPM	11.08 RPM
SRP007412_kidney	0.00 RPM	18.07 RPM
SRP007412_liver	0.00 RPM	23.57 RPM
SRP007412_testis	0.00 RPM	42.36 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_602 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_602 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_602 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_706

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005265	1 retrocopy	retro_btau_1095,
Canis familiaris	ENSCAFG00000008703	2 retrocopies	retro_cfam_1547, retro_cfam_675,
Choloepus hoffmanni	ENSCHOG00000005268	3 retrocopies	retro_chof_140, retro_chof_2143, retro_chof_268,
Callithrix jacchus	ENSCJAG00000019486	4 retrocopies	retro_cjac_1236, retro_cjac_2906, retro_cjac_3528, retro_cjac_909,
Echinops telfairi	ENSETEG00000003838	2 retrocopies	retro_etel_325, retro_etel_880,
Homo sapiens	ENSG00000131732	1 retrocopy	retro_hsap_1799,
Gorilla gorilla	ENSGGOG00000013790	1 retrocopy	retro_ggor_706,
Myotis lucifugus	ENSMLUG00000001886	1 retrocopy	retro_mluc_799,
Macaca mulatta	ENSMMUG00000020655	1 retrocopy	retro_mmul_797,
Mus musculus	ENSMUSG00000021621	1 retrocopy	retro_mmus_1920,
Otolemur garnettii	ENSOGAG00000002543	6 retrocopies	retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Pongo abelii	ENSPPYG00000015604	1 retrocopy	retro_pabe_1476,
Pan troglodytes	ENSPTRG00000017047	2 retrocopies	retro_ptro_1205, retro_ptro_602 ,
Rattus norvegicus	ENSRNOG00000014927	2 retrocopies	retro_rnor_1164, retro_rnor_2160,
Sorex araneus	ENSSARG00000008580	2 retrocopies	retro_sara_216, retro_sara_78,
Sarcophilus harrisii	ENSSHAG00000014504	1 retrocopy	retro_shar_734,
Ictidomys tridecemlineatus	ENSSTOG00000001407	2 retrocopies	retro_itri_422, retro_itri_696,
Tursiops truncatus	ENSTTRG00000013796	1 retrocopy	retro_ttru_819,