RetrogeneDB ID: retro_ggor_1418

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:61633782..61634638(-)
• Located in intron of: ENSGGOG00000006727

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC5
• Ensembl ID: ENSGGOG00000006803
• Aliases: None
• Description: None

Sequence

>retro_ggor_1418
GATGGACCAGAGCAGATGGAGCTGGAAGAGGGGAAGACAGGCAACAGACTCTGCCAGTATTATCTGTCTGAGACTGAAGA
ACTCCAGTCAGTAGTGAATGATAAGAGCCAGGACCTCCAGAGGCTGCAGGCATAAATGAATGAACTCAGTGCAGAAGTTC
ACCTATTGCAGGAGGAGCTACAGCTGCTGCAGGAACAGGGCTCCTGTGTAAGGGAAGTAGTCTGGGCCATGAATAAGGAG
AAGGTGTTAGTCAAGGTGTATCCCAAGGGCAAGTTTGTCTTAGATGTGGACAGAAACAGCGACATCAATGACATGAGACC
CAGTTGCCAGGGGGGCGCTAAGAAATGATAGCGACACACTGCACAATATCATACCCAGCAAAGTAGACCCACTGGTGTCA
CCAGTGATGGTGGAGAAGGTGCCAACCTTGATTTAAGAGATGATTGGTGGACTGGACAAGCAGATTAAGGACATCACAGA
AGTGATCGAGCCGCCTGTTAAGCATCCCAAGCTCTTTGAAGCACTGGGTATCACACAGCCCAGGGTGGTACTGCTGTACA
GACCTCTAGGCACTGGGAAGACACTATTTGCCTAGGCCGTGGCTCACCATACAGACTGTACCTTTGTTCATATCCCTGGC
TCTGAATTTGTATAGAAATTCATTGGGGAAGGGCCAAGAATGGTGAGGGAGCTGTTTGTCACGGCATGAGGACCTGCCAT
CTGTCTCATCAGCTCCATCAGCTCCTCGCAGCTGGAGGGGGGTTCTGGAGGGGACAGTGAAGTGCTGCACATCGTGCTGG
AACTGCTCAACCAACTGGACAGCTTTGAGGCCCCCAAGAAGATCAAGGTTATCATG

Alignment

ORF - retro_ggor_1418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.82 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLREELQLLQEQGSYV
          DGPEQMELEEGK.G..L.QYYLS..EELQ..VNDKSQ.L.RLQA..NEL.A.V.LL.EELQLLQEQGS.V
Retrocopy DGPEQMELEEGKTGNRLCQYYLSETEELQSVVNDKSQDLQRLQA*MNELSAEVHLLQEELQLLQEQGSCV

Parental  GEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNC-RVALRNDSYTLHKILPNKVDPLVSLMMVEK
          .EVV.AM.K.KVLVKV.P.GKFV.DVD.N.DIND..P.C.R.ALRNDS.TLH.I.P.KVDPLVS..MVEK
Retrocopy REVVWAMNKEKVLVKVYPKGKFVLDVDRNSDINDMRPSC>RGALRNDSDTLHNIIPSKVDPLVSPVMVEK

Parental  VPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFI
          VP....EMIGGLDKQIK.I.EVIE.PVKHP.LFEALGI.QP..VLLY.P.GTGKTL.A.AVAHHTDCTF.
Retrocopy VPTLI*EMIGGLDKQIKDITEVIEPPVKHPKLFEALGITQPRVVLLYRPLGTGKTLFA*AVAHHTDCTFV

Parental  RVSGSELVQKFIGEGARMVRELFVMAREHAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDG
          ...GSE.V.KFIGEG.RMVRELFV.A....P.I.....I.S...S.LEGGSGGDSEV....LELLNQLD.
Retrocopy HIPGSEFV*KFIGEGPRMVRELFVTA--*GPAICLISSISS---SQLEGGSGGDSEVLHIVLELLNQLDS

Parental  FEATKNIKVIM
          FEA.K.IKVIM
Retrocopy FEAPKKIKVIM

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	0.14 RPM	188.51 RPM
SRP007412_cerebellum	0.43 RPM	121.11 RPM
SRP007412_heart	0.28 RPM	81.02 RPM
SRP007412_kidney	0.65 RPM	169.32 RPM
SRP007412_liver	0.16 RPM	69.16 RPM
SRP007412_testis	0.00 RPM	172.80 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_1418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1418 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1949
Macaca mulatta	retro_mmul_1354

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002393	1 retrocopy	retro_dnov_1508,
Homo sapiens	ENSG00000087191	1 retrocopy	retro_hsap_1949,
Gorilla gorilla	ENSGGOG00000006803	1 retrocopy	retro_ggor_1418 ,
Macaca mulatta	ENSMMUG00000016769	1 retrocopy	retro_mmul_1354,
Monodelphis domestica	ENSMODG00000009873	2 retrocopies	retro_mdom_1411, retro_mdom_1583,
Nomascus leucogenys	ENSNLEG00000004150	1 retrocopy	retro_nleu_1480,
Oryctolagus cuniculus	ENSOCUG00000004329	1 retrocopy	retro_ocun_78,
Otolemur garnettii	ENSOGAG00000008296	1 retrocopy	retro_ogar_911,
Procavia capensis	ENSPCAG00000002653	1 retrocopy	retro_pcap_352,
Pongo abelii	ENSPPYG00000008533	1 retrocopy	retro_pabe_1606,
Pan troglodytes	ENSPTRG00000009525	1 retrocopy	retro_ptro_1303,
Ictidomys tridecemlineatus	ENSSTOG00000008945	1 retrocopy	retro_itri_1046,
Tupaia belangeri	ENSTBEG00000010546	3 retrocopies	retro_tbel_1411, retro_tbel_2422, retro_tbel_3450,
Tursiops truncatus	ENSTTRG00000006984	1 retrocopy	retro_ttru_1532,