RetrogeneDB ID: retro_mdom_1534

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:151091465..151092183(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A16
• Ensembl ID: ENSMODG00000017305
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; Graves disease autoantigen), member 16 [Source:HGNC Symbol;Acc:10986]

Sequence

>retro_mdom_1534
TTGGCTGCCCCATCTGCCCCTGAGGCTGGAGGAGCCAGAGGAGTTGGAGCTGGGAGTCCCAGCCTACCACCACATGTGTC
CACTCACAGGGACTTCTACTGTTTGCACTCCTTAATGACTGGAGGTATCATAGGATGTTAAGCCAAAACAACCATCATAC
CTTTGGATTGAGTGAAGCTACAATTGCAGGCACATAATCACCATTAAAAACATTTAGGAATATTTTCTGCCTTGTGAGCT
GTCCCTAAAAAAGACAGGTATCTTGGATTGTATAAAGGAAATGGTGCAATGATTAGAATCTTCCCATATGGTGCAATTCA
ATTTATGTTCTTTAACCATTAAAAAAAATTAATTACTAACAAACCTGGGATTTCTAAACAAGTATATTGGCTAATGGCTG
GCTCCATTGCAAGCATGACAGCAGTCATTTGTACTTATGTACTTGACATGGTTAGAGTTTACCAGGCATTTCAGGTGAAA
GGAGAACACACAGGTATTGGCTGTGCATTCAGAACAATTTATGCAAAGGAAGGTAGCTCATGTGAGTTTTACAGAGGACT
GATGCCTACTATTGTAGGAGAGACTCCCTACCAGGAGTTCAATTTTTTTTACTTTTGGTACCTTAAAGAGCGTTGGTCTC
TCTCACACTCCAACCTTGCTTGGAAGACCTTCATCAGTCAACCCTAGTGTCTTTGTTTTGAAAAAGCACATTAACTTG

Alignment

ORF - retro_mdom_1534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.49 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVAALAATGAGGAGAGSPSPPPAASARRDFYWLRSFVAGGIAGCCAKTTIAPLDRVKILLQAHNRHYK
          .AA..A..A.GA.G.GAGSPS.PP..S..RDFY.L.S...GGI.GC.AKTTI.PLD.VK..LQAHN.H.K
Retrocopy LAAPSAPEAGGARGVGAGSPSLPPHVSTHRDFYCLHSLMTGGIIGC*AKTTIIPLD*VKLQLQAHNHH*K

Parental  HLGVFSTLCAVPKKEGFLGLYKGNGAMMIRIFPYGAIQFMSFDHYKKIITTKLGISGHVHRLMAGSMAGM
          HLG.FS.L.AVPKK...LGLYKGNGAM.IRIFPYGAIQFM.F.H....IT.K.GIS..V..LMAGS.A.M
Retrocopy HLGIFSAL*AVPKKDRYLGLYKGNGAM-IRIFPYGAIQFMFFNHXXXLITNKPGISKQVYWLMAGSIASM

Parental  TAVICTYPLDMVRVRLAFQVKGEHTYTGIVHAFKTIYAKEGGFLGFYRGLMPTIIGMAPYAGVSFFTFGT
          TAVICTY.LDMVRV..AFQVKGEH..TGI..AF.TIYAKEG....FYRGLMPTI.G..PY..........
Retrocopy TAVICTYVLDMVRVYQAFQVKGEH--TGIGCAFRTIYAKEGSSCEFYRGLMPTIVGETPYQEFXXXXXXY

Parental  LK-SVGLTHAPTLLGRPSSDNPNVLVLKTHINL
          LK.SVGL.H.PTLLGRPSS.NP.V.VLK.HINL
Retrocopy LK>SVGLSHTPTLLGRPSSVNPSVFVLKKHINL

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	43.51 RPM
SRP007412_cerebellum	0.00 RPM	64.31 RPM
SRP007412_heart	0.00 RPM	35.68 RPM
SRP007412_kidney	0.00 RPM	92.18 RPM
SRP007412_liver	0.00 RPM	66.46 RPM
SRP007412_testis	0.00 RPM	28.29 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1534 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1534 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.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013726	1 retrocopy	retro_cfam_1092,
Myotis lucifugus	ENSMLUG00000015241	2 retrocopies	retro_mluc_1399, retro_mluc_2012,
Monodelphis domestica	ENSMODG00000002023	1 retrocopy	retro_mdom_1935,
Monodelphis domestica	ENSMODG00000017305	1 retrocopy	retro_mdom_1534 ,
Otolemur garnettii	ENSOGAG00000011191	1 retrocopy	retro_ogar_1291,
Ochotona princeps	ENSOPRG00000002758	1 retrocopy	retro_opri_1003,
Sus scrofa	ENSSSCG00000022303	1 retrocopy	retro_sscr_1000,
Vicugna pacos	ENSVPAG00000011819	1 retrocopy	retro_vpac_630,