RetrogeneDB ID: retro_ggor_1993

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:162115190..162116502(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSGGOG00000010620
• Aliases: None
• Description: None

Sequence

>retro_ggor_1993
ATGGATGAAAGTCAGAGTGGGGGTTATGGTCCTGGAGTTTGCAAGAAGAATGACAGGACAAGAAAAATAAATATGAACCT
CCTGTACCAACTAGAGTGGAGAAGAAGAAAACAAAGGGACCAGATGCTGCCAGCAAACTGCCACTGGTGACATCTCACAC
TCAGTGCTGATGAAAATTACTGAAGTTAGAGAGAATTGAAGACTGTCTTCTCATGGAGGAAGAATTCATTAGAAATCAGA
AATAAATGAAACCACTAGAAGAAAAGCAACAGAAAAGATTAAAAGTGGATGATCTGAGGGGGGACCCCAATAGCAGTAGG
AACCTTGGAAGAGATCACAATCATGCCATTATTCTACATCTGTGGGCTCAGAACACTACATCAGCATTCTTTCATTTGTA
GACAAGGATCTGCTGGAATCTGGCTGCTCGGTTCTGCTCAGCCACAAGGTGCATGCAGTGATAGGGGTGCTGATGGATGA
CACGGATCCCCTAGTCACAGTGATGAAGGTGGAAAAGACTCCCCAGGAGACCTATGCTGATACTGGGGGAAAAGTTGGAC
AACCACATTCAGGAAATTAAGGAATCTGTGGAGCCTCCTCTCACCCAACCTGAATATTATGAAGAGATGGGTGTAAAGCC
TCCTACGGGGTGGGGGGTCATTCTCTATGGTCCACCTGGCACAGGTAGAACCTTGTAGCCAAAGCGGTAGCAAACCAAAC
CTCAGCCACTTTCTTGAGAGTGGTTGGCTCTGAACTTATTCAGAAGTACCTGGGTGATGGGCTCAAACTCATACTGGAAT
TGTTTCAAGTTGCTGAAGAACACGCACCATCCACTGTGTTTATTGATGATATTAATGCCACTGGGACAAAAAGATATGAC
TCAAATTCTGGTGGTGAGATAGCAATTCAGGGAACAACGTTGGAACTGTGGAACCAGTTGGATGGATTTGATTCTAGGGG
AGATGTGAAAGTTATCATGGCCGCAAACCAAACAGAAATTTGGATCCAGCACTTAGCAGACCAGGCCGCACTGACAGGAA
GATCGGGATTCCCCTCCCTAATGAAAATACTAAGAAGAGCATCTTTCAGATTCATACAAGCATGATGACGCTGGCCAATG
ATGTAAACCTGGACGACTTGATAATGACTAAAGATGACCTCTTTGGTGCTGACATCAAGGCAATCTGCACAGAAGCTTGC
CTGATGGCCTTAAGAGAGCCACAGAATGAAGGTAACAAATGGAGACTTCAAAAAATATAAAGAAAATGTTCTTTGCAAAA
AACAGGAAGGCACTCCCAAAGGGCTCTATCTC

Alignment

ORF - retro_ggor_1993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MGQSQSGGHGPGGGKKDDK-DKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRLKLLKLERIK
          M..SQSGG.GPG..KK.D..DKK.KYEPPVPTRV...KKKTKGPDAASKLPLVT.HTQC..KLLKLERI.
Retrocopy MDESQSGGYGPGVCKKNDR<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  VDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKA-PQETYADIGG-LDNQIQEIKESVELPLT
          VDKDLLE.GCSVLL.HKVHAVIGVLMDDTDPLVTVMKVEK..P.......G..LDN.IQEIKESVE.PLT
Retrocopy VDKDLLESGCSVLLSHKVHAVIGVLMDDTDPLVTVMKVEKT>PRRPMLILGEKLDNHIQEIKESVEPPLT

Parental  HPEYYEEMGIKPPKG--VILYGPPGTGKTL-LAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRV
          .PEYYEEMG.KPP.G..VILYGPPGTG.TL..AKAVANQTSATFLRVVGSELIQKYLGDG.KL..ELF.V
Retrocopy QPEYYEEMGVKPPTGWGVILYGPPGTGRTL<VAKAVANQTSATFLRVVGSELIQKYLGDGLKLILELFQV

Parental  AEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-TLDPALI
          AEEHAPS.VFID.I.A.GTKRYDSNSGGE..IQ.T.LEL.NQLDGFDSRGDVKVIMA.N..E..LDPAL.
Retrocopy AEEHAPSTVFIDDINATGTKRYDSNSGGEIAIQGTTLELWNQLDGFDSRGDVKVIMAANQTE<NLDPALS

Parental  RPGRIDRKIEFPLPDEKTKKHIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRE-RR
          RPGR.DRKI..PLP.E.TKK.IFQIHTS.MTLA.DV.LDDLIM.KDDL.GADIKAICTEA.LMALRE..R
Retrocopy RPGRTDRKIGIPLPNENTKKSIFQIHTSMMTLANDVNLDDLIMTKDDLFGADIKAICTEACLMALRE>HR

Parental  MKVTNEDFKKSKENVLYKKQEGTPEGLYL
          MKVTN.DFKK.KENVL.KKQEGTP.GLYL
Retrocopy MKVTNGDFKKYKENVLCKKQEGTPKGLYL

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	0.43 RPM	84.11 RPM
SRP007412_cerebellum	0.28 RPM	52.64 RPM
SRP007412_heart	0.03 RPM	38.62 RPM
SRP007412_kidney	0.12 RPM	73.60 RPM
SRP007412_liver	0.16 RPM	41.78 RPM
SRP007412_testis	0.73 RPM	111.47 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1993 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1993 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2873
Pan troglodytes	retro_ptro_1944
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,