RetrogeneDB ID: retro_mdom_530

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:182111523..182112489(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBQLN4
• Ensembl ID: ENSMODG00000016961
• Aliases: None
• Description: ubiquilin 4 [Source:HGNC Symbol;Acc:1237]

Sequence

>retro_mdom_530
GAGAACATCTTTGTCCAAGACGTGATGTCCAACCCTGACCTGTTGTGCCACATGATCATGGCCAACCCACAGATACAAAG
CTGTTGGAGAGGAATCTAGATTTCAGCCATATGCTCAATAACCCACAAATAATGAGATAGACCATGGAATTGGCTTTGAA
GCCCCAACATGATGCAGGAGATAATGTGCAACCCAGACTAGGCTCTGAGCAACCTACAGAGCATCTCAGGAGATGCAATG
GCTTGTGTTGCATGTACTCAGACACACAAGAACCCATATTCAATGCTGCTAGAGAACAATTTAGTAATGATCCCTTCTCC
TTATTGGTTAGGAACTCTGACAGCTCCTTCTCCCAACCTCTCTAGGACTGAGAACTTTCCCAAGCCCCAGGGGCCCCATC
AGCTCTCACTTCCCAGGACCCAGAGCCCATTGGGCAGAATCCAGAGGCTCACAGACCAGCCAGGTGAACCCCAACAGTTT
CTATCCTTTGGAGATCCATGCAGCCTGGGATCAGAGATGTTTAATAACCCCGAGATACCCAGCCTTCTCCAGCAAATTTC
AGTAAATCTCCAGCGAATGAAAAACATGATCTTTGTCCCATATGTGCAAATATGATGCAGACATTTACCCAGAACTCTGA
TTTTGCTGCTTAGATGCTGATGTACATTCCTTTGTTTGTGGGAAACCCCCAGCTGCAGGAATAGTTCTGGCTTCGTCCCT
GTCTTTTGAAAGAAGCCCCAACCCAAGACCCAGACTTTCTGTCTATTCTCACCAACCCCTGGGACATACAGGTCCTGCTA
CAGATCCAACAGGGACTGCAGAGGCTGTAGATGAAAGCCCTAGGGCTAGTGCCCAGCAGTGGCAACTTTGGGGCCCTCCA
GATTCTACACCCCATGGAGGAAGTAGTAGCGCCCCTACAGAGCCCATCACTTCCCATCCATTCCAGCTAGAGCCTCTGGG
GGCACA

Alignment

ORF - retro_mdom_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.23 %
• Parental protein coverage: 54.17 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  ENPLVQDMMSNPDLMRHMIMANPQMQ-QLMERNPEISHMLNNPELMRQTMELARNPA-MMQEMMRNQDRA
          EN..VQD.MSNPDL..HMIMANPQ.Q..L.ERN...SHMLNNP..MR.TMELA..P..MMQE.M.N.D.A
Retrocopy ENIFVQDVMSNPDLLCHMIMANPQIQ<KLLERNLDFSHMLNNPQIMR*TMELALKPQ>MMQEIMCNPD*A

Parental  LSNLESIPGGY-NALRRMYTDIQEPMFSAAREQFGNNPFSSLAGNSDSSSSQPL-RTENREPLPNPWSPS
          LSNL.SI.G...N.L..MY.D.QEP.F.AAREQF.N.PFS.L..NSDSS.SQPL.RTEN......P...S
Retrocopy LSNLQSISGDA<NGLCCMYSDTQEPIFNAAREQFSNDPFSLLVRNSDSSFSQPL>RTENFPKPQGPHQLS

Parental  APTSQ-APGEGTGGSGTSQVHPTVSNP-FGINAASLGSGMFNSPEMQGLLQQISENPQLMQNMISAPYMR
          .P..Q.A......GS.TSQV.P....P.FG....SLGS.MFN.PE...LLQQIS.N.Q.M.NMI..PY..
Retrocopy LPRTQ>AHWAESRGSQTSQVNPNSFYP<FG-DPCSLGSEMFNNPEIPSLLQQISVNLQRMKNMIFVPYVQ

Parental  -SMMQTLAQNPDFAAQMMVNVPLFAGNPQLQEQLRLQLPVFLQQM--QNPDSLSILTNPRAMQALLQIQQ
          ..MMQT..QN.DFAA.M....PLF.GNPQLQE...L..P..L.....Q.PD.LSILTNP...Q.LLQIQQ
Retrocopy <NMMQTFTQNSDFAA*MLMYIPLFVGNPQLQE*FWLR-PCLLKEAPTQDPDFLSILTNPWDIQVLLQIQQ

Parental  GLQTLQTEAPGLVPSLGNFGA-PRIPPPPAGGSSSQEPPITS-PSTPASASPVGGT
          GLQ.L...A.GLVPS.GNFGA.P....P..G.SS....PITS.PS.PA.AS..GGT
Retrocopy GLQRL*MKALGLVPSSGNFGA<PPDSTPHGGSSSAPTEPITS<PSIPARAS--GGT

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_530 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_530 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160803	1 retrocopy	retro_hsap_2859,
Gorilla gorilla	ENSGGOG00000008916	1 retrocopy	retro_ggor_26,
Macropus eugenii	ENSMEUG00000016573	1 retrocopy	retro_meug_109,
Microcebus murinus	ENSMICG00000002222	1 retrocopy	retro_mmur_1146,
Macaca mulatta	ENSMMUG00000009983	1 retrocopy	retro_mmul_905,
Monodelphis domestica	ENSMODG00000016961	1 retrocopy	retro_mdom_530 ,
Pan troglodytes	ENSPTRG00000001444	1 retrocopy	retro_ptro_1934,