RetrogeneDB ID: retro_ptro_1944

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:165113435..165114746(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSPTRG00000006623
• Aliases: None
• Description: None

Sequence

>retro_ptro_1944
ATGGGTGAAAGTCAGAGTGGGGGTTATGGTCCTGGAGTTTGCAAGAAGAATGACAGGACAAGAAAAATAAATATGAACCT
CCTGTACCAACTAGAGTGGAGAAGAAGAAAACAAAGGGACCAGATGCTGCCAGCAAACTGCCACTGGTGACATCTCACAC
TCAGTGCTGATGAAAATTACTGAAGTTAGAGAGAATTGAAGACTGTCTTCTCATGGAGGAAGAATTCATTAGAAATCAGA
AATAAATGAAACCATTAGAAGAAAAGCAACAGAAAAGATTAAAAGTGGATGATCTGAGGGGGGACCCCAATAGCAGTAGG
AACCTTGGAAGAGATCACAATCATGCCATTATTCTACATCTGTGGGCTCAGAACACTACATCAGCATTCTTTCATTTGTA
GACAAGGATCTGCTGGAACCTGGCTGCTCGGTTCTGCTCAGCCACAAGGTGCATGCAGTGATAGGGGTGCTGATGGATGA
CACGGATCCCCTAGTCACAGTGATGAAGGTGGAAAAGACTCCCCAGGAGACTATGCTGATACTGGGAGAAAAGTTGGACA
ACCAAATTCAGGAAATTAAGGAATCTGTGGAGCCTCCTCTCACCCAACCTGAATATTATGAAGAGACGGGTGTAAAGCTT
CCTACGGGGTGGGGGGTCATTCTCTATGGTCCACCTGGCACAGGTAGAACCTTGTAGCCAAAGCGGTAGCAAACCAAACC
TCAGCCACTTTCTTGAGAGTGGTTGGCTCTGAACTTATTCAGAAGTACCTGGGTGATGGGCTCAAACTCATACTGGAATT
GTTTCAAGTTGCTGAAGAACACGCACCATCCACTGTGTTTATTGATGATATTAATGTCACTGGAACAAAAAGATATGACT
CAAATTCTGGTGGTGAGATAGCAATTCAGCGAACAATGTTGGAACTGTGGAACCAGTTGGATGGATTTGATTCTAGGGGA
GATGTGAAAGTTATCATGGCCGCAAAGCAAACAGAAATTTGGATCCAGCACTTAGCAGACCAGGCCGCACTGACAGGAAG
ATCGGGATTCCCCTCCCTAATGAAAATACTAAGAAGAGCATCTTTCAGATGCATACAAGCATGATGACACTGGCCGATGA
TGTAAACCTGGACGACTTGATAATGACTAAAGATGACCTCTTTGGTGCTGACATCAAGGCAATCTGCACAGAAGCTTGCC
TGATGGCCTTAAGAGAGCCACAGAACGAAGGTAACAAATGAAGACTTCAAAAAATATAAAGAAAATGTTCTTTGCAAAAA
ACAGGAAGGCACTCCCAAGGGGCTCTATCTC

Alignment

ORF - retro_ptro_1944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGQSQSGGHGPGGGKKDDK-DKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRLKLLKLERIK
          MG.SQSGG.GPG..KK.D..DKK.KYEPPVPTRV...KKKTKGPDAASKLPLVT.HTQC..KLLKLERI.
Retrocopy MGESQSGGYGPGVCKKNDR<DKKNKYEPPVPTRV--EKKKTKGPDAASKLPLVTSHTQC**KLLKLERIE

Parental  DYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIV-STSVGSEHYVSILSF
          D.LLMEEEFIRNQ..MKPLEEKQ...R.KVDDLRG.P.S...L....D.NHAI..STSVGSEHY.SILSF
Retrocopy DCLLMEEEFIRNQK*MKPLEEKQQK-RLKVDDLRGDPNSSRNLGR--DHNHAII<STSVGSEHYISILSF

Parental  VDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGG-LDNQIQEIKESVELPLTH
          VDKDLLEPGCSVLL.HKVHAVIGVLMDDTDPLVTVMKVEK.PQET....G..LDNQIQEIKESVE.PLT.
Retrocopy VDKDLLEPGCSVLLSHKVHAVIGVLMDDTDPLVTVMKVEKTPQETMLILGEKLDNQIQEIKESVEPPLTQ

Parental  PEYYEEMGIKPPKG--VILYGPPGTGKTL-LAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVA
          PEYYEE.G.K.P.G..VILYGPPGTG.TL..AKAVANQTSATFLRVVGSELIQKYLGDG.KL..ELF.VA
Retrocopy PEYYEETGVKLPTGWGVILYGPPGTGRTL<VAKAVANQTSATFLRVVGSELIQKYLGDGLKLILELFQVA

Parental  EEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-TLDPALIR
          EEHAPS.VFID.I...GTKRYDSNSGGE..IQRTMLEL.NQLDGFDSRGDVKVIMA....E..LDPAL.R
Retrocopy EEHAPSTVFIDDINVTGTKRYDSNSGGEIAIQRTMLELWNQLDGFDSRGDVKVIMAAKQTE<NLDPALSR

Parental  PGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRE-RRM
          PGR.DRKI..PLP.E.TKK.IFQ.HTS.MTLADDV.LDDLIM.KDDL.GADIKAICTEA.LMALRE..R.
Retrocopy PGRTDRKIGIPLPNENTKKSIFQMHTSMMTLADDVNLDDLIMTKDDLFGADIKAICTEACLMALRE>HRT

Parental  KVTNEDFKKSKENVLYKKQEGTPEGLYL
          KVTNEDFKK.KENVL.KKQEGTP.GLYL
Retrocopy KVTNEDFKKYKENVLCKKQEGTPKGLYL

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	0.04 RPM	62.60 RPM
SRP007412_cerebellum	0.04 RPM	71.37 RPM
SRP007412_heart	0.00 RPM	89.42 RPM
SRP007412_kidney	0.00 RPM	64.20 RPM
SRP007412_liver	0.03 RPM	80.20 RPM
SRP007412_testis	10.54 RPM	139.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1944 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1944 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1944 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2873
Gorilla gorilla	retro_ggor_1993
Pongo abelii	retro_pabe_2379
Callithrix jacchus	retro_cjac_1537

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017510	2 retrocopies	retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni	ENSCHOG00000013595	1 retrocopy	retro_chof_1954,
Callithrix jacchus	ENSCJAG00000017701	7 retrocopies	retro_cjac_1152, retro_cjac_1537, retro_cjac_2417, retro_cjac_2433, retro_cjac_4219, retro_cjac_661, retro_cjac_678,
Dasypus novemcinctus	ENSDNOG00000006458	1 retrocopy	retro_dnov_2162,
Homo sapiens	ENSG00000100764	10 retrocopies	retro_hsap_1090, retro_hsap_1278, retro_hsap_2080, retro_hsap_2658, retro_hsap_2810, retro_hsap_2873, retro_hsap_3323, retro_hsap_3416, retro_hsap_3793, retro_hsap_975,
Gorilla gorilla	ENSGGOG00000010620	8 retrocopies	retro_ggor_1004, retro_ggor_1298, retro_ggor_1629, retro_ggor_1954, retro_ggor_1993, retro_ggor_2309, retro_ggor_780, retro_ggor_858,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
Microcebus murinus	ENSMICG00000016733	7 retrocopies	retro_mmur_1039, retro_mmur_1063, retro_mmur_1245, retro_mmur_1577, retro_mmur_216, retro_mmur_839, retro_mmur_983,
Macaca mulatta	ENSMMUG00000022990	1 retrocopy	retro_mmul_255,
Nomascus leucogenys	ENSNLEG00000017013	10 retrocopies	retro_nleu_1123, retro_nleu_1163, retro_nleu_1589, retro_nleu_1625, retro_nleu_1669, retro_nleu_2318, retro_nleu_2625, retro_nleu_429, retro_nleu_616, retro_nleu_706,
Oryctolagus cuniculus	ENSOCUG00000006231	4 retrocopies	retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii	ENSOGAG00000032343	2 retrocopies	retro_ogar_3014, retro_ogar_367,
Pongo abelii	ENSPPYG00000025948	9 retrocopies	retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pan troglodytes	ENSPTRG00000006623	9 retrocopies	retro_ptro_1530, retro_ptro_1904, retro_ptro_1944 , retro_ptro_2153, retro_ptro_2321, retro_ptro_2573, retro_ptro_672, retro_ptro_742, retro_ptro_874,