RetrogeneDB ID: retro_mdom_868

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:253707183..253708506(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC2
• Ensembl ID: ENSMODG00000017238
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 2 [Source:HGNC Symbol;Acc:9548]

Sequence

>retro_mdom_868
ACCGAGGTAGCTACGAGTCCCAAAATGCCGGATTACCTAGGCGCTGATCAGCGGAAAACCAAAGAAGAGGAGAAGGATGA
TAAACCCATCCGAGCACTGGATGAAGGTGATATTGCCTTGTTGAAAACTTACGGCCAGAGTACTTATTCTAGACAGATCA
AGCAAGTAGAAGATGATATCCAGCAACTTCTTAAGAAAATCAATGAGCTCACTGGCATTAAAGAGTCAGATACTGGCTTG
GCTCCCCCAGCTCTTTGGGATTTGGCTGCAGATAAACAGACCCTTCAGAGTGAACAGCCCCTGCAGGTTGCGAGGTGTAC
AAAGATAATCAATGCTGATTCAGAGGACCCAAAATACATTATCAACGTGAAACAGTTTGCCAAATTTGTGGTGGACCTTA
GTGATCAGGTAGCACCCACTGACATTGAAGAAGGAATGAGAGTTGGTGTGGACAGAAATAAGTATCAAATTCATATTCCT
CTGTCTCCCAAGATTGACCCAACAGTTACCATGATGTAAGTGGAAGAAAAACCTGATGTCACATACAGTGATGTTGGTGG
TTGCAAAGAACAGATTGAGAAGCTACGAGAGGTGGTTGAAACTCCACTGCTTCATCCAGAGAGGTTTGTTAACCTTGGTA
TTGAACCCCCAAAAGGTGTGCTTCTTTTTGGTCCCCCAGGCACGGGCAAGACTCTTTGTGCTCGTGCTGTTGCAAACAGA
ACAGATGCCTGCTTCATCCGAGTTATTGGATCTGAACTTGTGCAGAAATATGTTGGAGAGGGGGCCCGAATGGTCCGTGA
GCTCTTTGAAATGGCTAGAACCAAAAAGGCCTGCCTTATATTCTTTGATGAAATTGATGCTATTGGAGGTGCTCGTTTTG
ATGTTGGAGCTGGGGGTGACAATGAAGTACAGAGAACCATGTTGGAACTTATCAATCAGTTGGATGGATTTGATCCTTGA
GGTAATATTAAAGTACTAATGGCTACCAACAGACCTGATACTTTGGACCCAGCATTAATGAGGCCCGGGAGACTGGATCG
AAAGATTGAATTTAGCTTACCTGATCTGGAGGGTCGGACACATATTTTCAAGATTCATGCTCGTTCAATGAGTGTTGAAA
GAGATATAAGATTTGAGTTGTTAGCACGGCTGTGTCCCAATAGCACTGGTGCTGAAATTAGAAGTGTTTGCACTGAAGCA
GGGATGTTTGCCATCAGAGCACGACGAAAAATTGCCACTGAGAAAGATTTCTTGGAAGCTGTGAATAAGGTCATTAAGTC
ATATGCCAAATTCAGTGCTACTCCTCGTTACATGACATACAAC

Alignment

ORF - retro_mdom_868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.09 %
• Parental protein coverage: 96.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TEVATSPKMPDYLGADQRKTKEEEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKINEL
          TEVATSPKMPDYLGADQRKTKEEEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKINEL
Retrocopy TEVATSPKMPDYLGADQRKTKEEEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKINEL

Parental  TGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAKFVVDLSDQVAPT
          TGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAKFVVDLSDQVAPT
Retrocopy TGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAKFVVDLSDQVAPT

Parental  DIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERFV
          DIEEGMRVGVDRNKYQIHIPL.PKIDPTVTMM.VEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERFV
Retrocopy DIEEGMRVGVDRNKYQIHIPLSPKIDPTVTMM*VEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERFV

Parental  NLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRVIGSELVQKYVGEGARMVRELFEMARTKKACLI
          NLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRVIGSELVQKYVGEGARMVRELFEMARTKKACLI
Retrocopy NLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRVIGSELVQKYVGEGARMVRELFEMARTKKACLI

Parental  FFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIE
          FFDEIDAIGGARFD.GAGGDNEVQRTMLELINQLDGFDP.GNIKVLMATNRPDTLDPALMRPGRLDRKIE
Retrocopy FFDEIDAIGGARFDVGAGGDNEVQRTMLELINQLDGFDP*GNIKVLMATNRPDTLDPALMRPGRLDRKIE

Parental  FSLPDLEGRTHIFKIHARSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEA
          FSLPDLEGRTHIFKIHARSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEA
Retrocopy FSLPDLEGRTHIFKIHARSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEA

Parental  VNKVIKSYAKFSATPRYMTYN
          VNKVIKSYAKFSATPRYMTYN
Retrocopy VNKVIKSYAKFSATPRYMTYN

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_868 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_868 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

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,