RetrogeneDB ID: retro_ggor_1885

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:132254844..132256137(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC2
• Ensembl ID: ENSGGOG00000009167
• Aliases: None
• Description: None

Sequence

>retro_ggor_1885
ATGCCAGATTACCTTGGTGCCCATCAGTGGAAGACCAAAGATGATGAGAAGGATGACAAGCCCATCCAAGTTCTGGATGA
GGCGGATATTGCCTTGCTGAAAACTTATGGTCAGAGCACTTACTTTAGGCAGATCAAGCAAGTCGAAGATGGCATTCAGC
AACTTCTCAAGAAAATTAATGAGCTCACTGGTATTAAAGAATCTGACACTGGCCTGGCTCCACCAGCACTCTGGGATTTG
GCTGCAGATAAGCAGACACTCCAGAGTAAACAGCCTTTACAGGTTGCCAGGTGTACAAAGATAATCAATGCTGATTCAGA
GGACCCAAAATACATTGTCAACGTAAAGCAGTTTGCCAAGTTTGTGATGGACTTTAGTGATCAGGTGGCACCCACTGACA
TTGAAGAAGGGATGAGAGTAGGTGTGGACAGAAATAAATATCAAATTCACATTCCATTGCCTCCTAAGACTCACCCAACA
GTTACCATGATGCAGGTGGAGGAAAAACCTGTCACATACAGTGATGTTGGTGACTGTAAGGAGCGATTGAGAAATTGCGA
GAAGTAGTTGAAACCCCATTACTTCATCCAGAGAGGTTTGTGAATCTTGGCATTGAGCCTCCCAAGGGCATGCTGCTCTT
TAATCCACCCAGTACAGGAAGACACTCTGTGTGTGGGCAGTTGCTAATCAGACTGATGCGTGCTTCATTCGAGTTACTGG
ATCTGAGCTGTACAGAAATATGTCAGTGAGAGGGCTCAAATGGTTCATGAGCTCTTTGAAATGACCAGAACAAAAAAAGC
CTGCCTTATCTTCTTTGATGAAATTGATGCTATTGGAGGGGCTCGGTTTGATGATGGTGCTAGAGATGACAATGAAGTGC
AGAGAACGATGCTGGAACTGATCAATCAGCTTGATGGTTTTGATCCTCGAGGCAATATTAAAGTGCTGATGGCCACTAAC
TGACCTGATAATTTGGATCCAGCACTGATGAGGCCAGGGAGATTAGATAGAAAAATTGAATTTAGCTTGCCCGATCTAGA
GGGTCGGACCCACATCTTTAAGATTCACGCTCATTCAATGAGTGTTGAAAGATATATCAGATTTGAATTGTTAGCATGAC
TGTGTCCAAATGGCACTGCTGCTGAGATTAGAAGTGTCTGCACAGAAGCTGGTATGTTTGCCATCAGAGCACGGCGAAAA
ATTGCTACTGAGAAGGATTTCTTGGAAGCTGTAAGTAAGGTCATTAAGTCTTATGCCAAATTCAGTGCTACTCCTCACTA
CATGACATACAAC

Alignment

ORF - retro_ggor_1885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKINELTGIKESDT
          MPDYLGA.Q.KTK.DEKDDKPI..LDE.DIALLKTYGQSTY.RQIKQVED.IQQLLKKINELTGIKESDT
Retrocopy MPDYLGAHQWKTKDDEKDDKPIQVLDEADIALLKTYGQSTYFRQIKQVEDGIQQLLKKINELTGIKESDT

Parental  GLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAKFVVDLSDQVAPTDIEEGMRV
          GLAPPALWDLAADKQTLQS.QPLQVARCTKIINADSEDPKYI.NVKQFAKFV.D.SDQVAPTDIEEGMRV
Retrocopy GLAPPALWDLAADKQTLQSKQPLQVARCTKIINADSEDPKYIVNVKQFAKFVMDFSDQVAPTDIEEGMRV

Parental  GVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQ-IEKLREVVETPLLHPERFVNLGIEPP
          GVDRNKYQIHIPLPPK..PTVTMMQVEEKP.VTYSDVG.CKE..IEKLREVVETPLLHPERFVNLGIEPP
Retrocopy GVDRNKYQIHIPLPPKTHPTVTMMQVEEKP-VTYSDVGDCKER<IEKLREVVETPLLHPERFVNLGIEPP

Parental  KGVLLFGPPGTG-KTLCARAVANRTDACFIRVIGSEL-VQKYVGEGARMVRELFEMARTKKACLIFFDEI
          KG.LLF.PP.TG.KTLC..AVAN.TDACFIRV.GSEL.VQKYV.E.A.MV.ELFEM.RTKKACLIFFDEI
Retrocopy KGMLLFNPPSTG<KTLCVWAVANQTDACFIRVTGSEL<VQKYVSERAQMVHELFEMTRTKKACLIFFDEI

Parental  DAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPD
          DAIGGARFDDGA..DNEVQRTMLELINQLDGFDPRGNIKVLMATN.PD.LDPALMRPGRLDRKIEFSLPD
Retrocopy DAIGGARFDDGARDDNEVQRTMLELINQLDGFDPRGNIKVLMATN*PDNLDPALMRPGRLDRKIEFSLPD

Parental  LEGRTHIFKIHARSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVI
          LEGRTHIFKIHA.SMSVER.IRFELLA.LCPN.T.AEIRSVCTEAGMFAIRARRKIATEKDFLEAV.KVI
Retrocopy LEGRTHIFKIHAHSMSVERYIRFELLA*LCPNGTAAEIRSVCTEAGMFAIRARRKIATEKDFLEAVSKVI

Parental  KSYAKFSATPRYMTYN
          KSYAKFSATP.YMTYN
Retrocopy KSYAKFSATPHYMTYN

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	0.05 RPM	48.82 RPM
SRP007412_cerebellum	0.04 RPM	37.66 RPM
SRP007412_heart	0.00 RPM	17.60 RPM
SRP007412_kidney	0.08 RPM	53.32 RPM
SRP007412_liver	0.03 RPM	36.48 RPM
SRP007412_testis	0.10 RPM	79.88 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_1885 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1885 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2705
Pan troglodytes	retro_ptro_1826
Pongo abelii	retro_pabe_2257

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005729	1 retrocopy	retro_etel_1316,
Homo sapiens	ENSG00000161057	2 retrocopies	retro_hsap_2705, retro_hsap_3980,
Gorilla gorilla	ENSGGOG00000009167	3 retrocopies	retro_ggor_1885 , retro_ggor_2672, retro_ggor_2673,
Myotis lucifugus	ENSMLUG00000008853	1 retrocopy	retro_mluc_1642,
Macaca mulatta	ENSMMUG00000003432	2 retrocopies	retro_mmul_1538, retro_mmul_2299,
Monodelphis domestica	ENSMODG00000017238	1 retrocopy	retro_mdom_868,
Mustela putorius furo	ENSMPUG00000018268	3 retrocopies	retro_mputfur_1025, retro_mputfur_232, retro_mputfur_387,
Nomascus leucogenys	ENSNLEG00000009274	2 retrocopies	retro_nleu_1578, retro_nleu_2042,
Otolemur garnettii	ENSOGAG00000005164	2 retrocopies	retro_ogar_2198, retro_ogar_2309,
Pongo abelii	ENSPPYG00000017883	2 retrocopies	retro_pabe_2257, retro_pabe_2412,
Pan troglodytes	ENSPTRG00000019553	2 retrocopies	retro_ptro_1826, retro_ptro_2702,
Tarsius syrichta	ENSTSYG00000000666	4 retrocopies	retro_tsyr_1031, retro_tsyr_1272, retro_tsyr_1857, retro_tsyr_2178,
Vicugna pacos	ENSVPAG00000008921	1 retrocopy	retro_vpac_44,