RetrogeneDB ID: retro_ptro_1826

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:135674351..135675645(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC2
• Ensembl ID: ENSPTRG00000019553
• Aliases: None
• Description: None

Sequence

>retro_ptro_1826
ATGCCAGATTACCTTGGTGCCCATCAGCGGAAGACCAAAGATGATGAGAAGGATGACAAGTCCATCCAAGTTCTGGATGA
GGCGGATATTGCCTTGCTGAAAACTTATGGTCAGAGCACTTACTTTAGGCAGATCAAGCAAGTCGAAGATGGCGTTCAGC
AACTTCTCAAGAAAATTAATGAGCTCACTGGTATTAAAGAATCTGACACTGGCCTGGCTCCACCAGCACTCTGGGATTTG
GCTGCAGATAAGCAGACACTCCAGAGGAAACAGCCTTTACAGGTTGCCAGGTGTACAAAGATAATCAATGCTGATTCAGA
GGACCCAAAATACATTGTCAACGTAAAGCAGTTTGCCAAGTTTGTGATGGACTTTAGTGATCAGGTGGCACCCACTGACA
TTGAAGAAGGGATGAGAGTAGGTGTGGACAGAAATAAATATCAAATTCACATTCCATTGCCTCCTAAGACTCACCCAACA
GTTACCATGATGCAGGTGGAGGAAAAACCTGTCACATACAGTGATGTTGGTGACTGTAAGGAGCAGATTGAGAAATTGCG
AGAAGTAGTTGAAACCCCATTACTTCATCCAGAGAGGTTTGTGAATCTTGGCATTGAGCCTCCCAAGGGCATGCTGCTCT
TTAATCCACCCAGTACAGGAAGACACTCTGTGTGTGGGCAGTTGCTAATCAGACTGATGCGTGCTTCATTCGAGTTATTG
GATCTGAGCTGTACAGAAATATGTCAGTGAGAGGGCTCAAATGGTTCATGAGCTCTTTGAAATGACCAGAACAAAAAAAG
CCTGCCTTATCTTCTTTGATGAAATTGATGCTATTGGAGGGGCTCGGTTTGATGATGGTGCTAGAGGTGACAATGAAGTG
CAGAGAACGATGTTGGAACTGATCAATCAGCTTGATGGTTTTGATCCTCGAGGCAATATTAAAGTGCTGATGGCCACTAA
CTGACCTGATAATTTGGATCCAGCACTGATGAGGCCAGGGAGATTAGATAGAAAAATTGAATTTAGCTTGCCTGATCTAG
AGGGTCGGACCCACATCTTTAAGATTCACGCACATTCAATGAGTGTTGAAAGATATATCAGATTTGAATTGTTAGCACGA
CTGTGTCCAAATGGCACTGCTGCTGAGATTAGAAGTGTCTGCACAGAAGCTGGTATGTTTGCCATCAGAGCACGGCGAAA
AATTGCTACTGAGAAGGATTTCTTGGAAGCTGTAAGTAAGGTCATTAAGTCTTATGCCAAATTCAGTGCTACTCCTCACT
ACATGACATACAAC

Alignment

ORF - retro_ptro_1826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKINELTGIKESDT
          MPDYLGA.QRKTK.DEKDDK.I..LDE.DIALLKTYGQSTY.RQIKQVED..QQLLKKINELTGIKESDT
Retrocopy MPDYLGAHQRKTKDDEKDDKSIQVLDEADIALLKTYGQSTYFRQIKQVEDGVQQLLKKINELTGIKESDT

Parental  GLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAKFVVDLSDQVAPTDIEEGMRV
          GLAPPALWDLAADKQTLQ..QPLQVARCTKIINADSEDPKYI.NVKQFAKFV.D.SDQVAPTDIEEGMRV
Retrocopy GLAPPALWDLAADKQTLQRKQPLQVARCTKIINADSEDPKYIVNVKQFAKFVMDFSDQVAPTDIEEGMRV

Parental  GVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERFVNLGIEPPK
          GVDRNKYQIHIPLPPK..PTVTMMQVEEKP.VTYSDVG.CKEQIEKLREVVETPLLHPERFVNLGIEPPK
Retrocopy GVDRNKYQIHIPLPPKTHPTVTMMQVEEKP-VTYSDVGDCKEQIEKLREVVETPLLHPERFVNLGIEPPK

Parental  GVLLFGPPGTG-KTLCARAVANRTDACFIRVIGSEL-VQKYVGEGARMVRELFEMARTKKACLIFFDEID
          G.LLF.PP.TG.KTLC..AVAN.TDACFIRVIGSEL.VQKYV.E.A.MV.ELFEM.RTKKACLIFFDEID
Retrocopy GMLLFNPPSTG<KTLCVWAVANQTDACFIRVIGSEL<VQKYVSERAQMVHELFEMTRTKKACLIFFDEID

Parental  AIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDL
          AIGGARFDDGA.GDNEVQRTMLELINQLDGFDPRGNIKVLMATN.PD.LDPALMRPGRLDRKIEFSLPDL
Retrocopy AIGGARFDDGARGDNEVQRTMLELINQLDGFDPRGNIKVLMATN*PDNLDPALMRPGRLDRKIEFSLPDL

Parental  EGRTHIFKIHARSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIK
          EGRTHIFKIHA.SMSVER.IRFELLARLCPN.T.AEIRSVCTEAGMFAIRARRKIATEKDFLEAV.KVIK
Retrocopy EGRTHIFKIHAHSMSVERYIRFELLARLCPNGTAAEIRSVCTEAGMFAIRARRKIATEKDFLEAVSKVIK

Parental  SYAKFSATPRYMTYN
          SYAKFSATP.YMTYN
Retrocopy SYAKFSATPHYMTYN

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	0.20 RPM	42.11 RPM
SRP007412_cerebellum	0.00 RPM	68.00 RPM
SRP007412_heart	0.06 RPM	72.40 RPM
SRP007412_kidney	0.03 RPM	56.33 RPM
SRP007412_liver	0.16 RPM	70.38 RPM
SRP007412_testis	0.53 RPM	104.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1826 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1826 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1826 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2705
Gorilla gorilla	retro_ggor_1885
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,