RetrogeneDB ID: retro_mdom_1866

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:146823869..146824498(+)
• Located in intron of: ENSMODG00000017022

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM8A1
• Ensembl ID: ENSMODG00000024641
• Aliases: None
• Description: family with sequence similarity 8, member A1 [Source:HGNC Symbol;Acc:16372]

Sequence

>retro_mdom_1866
GCTGCCCCTGCCTCCATGGCTTTGGCTTCTGCTGCTACTACACTCTCTGGGGAGTCCCCAGACTCCCATCTTGCAGGGAT
TACACAGATTAGCTCCAGTGGGCATGGCTGGAGGGGCCCCAGCACTTGGGCAGTAGAGTTAGAAAACTCATCCTGTAGGC
ACAGAATATGCTGTTTCCATCTTTGGCACACGGGTTTAAGGCAGAGATGGTGCATTTCTTTATTCTAGACTTTTATAAAA
GTAACCGTGGTCTTAACTATTATGCATGTCAGTGAAATAAAGAATATTTCTGAGTTTGCTATCTATTACATGATAGAAGA
ACTAGATGAAGATGCATCAATGCAAGACGTGCAGAAAATCATTATTAGGGCTCTTGTATTCAGGTTATTAGTTTGTGTTG
ATGAGATAATTTGTATATCAGAAGGGAGTGGAGCACTCCAGGGAAATTTTTGCTGGGGCTTCATGTCATGACATATGATA
CATCAGAATTTATTGCACCAAGCAATGTTTTAGTGATTCATTCCTCAAATGTTAATATAACAATGTCCATTATTTGAGCT
TATGTTTCTATTGCTTCTTTTCCCCCTGTTTTCATCAGACTACTCTCTTTTCAGCATAATCAAACAGCC

Alignment

ORF - retro_mdom_1866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.19 %
• Parental protein coverage: 50.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AAAAAAAAAAAAAAPSPGA-RAPNWQGSARIAPVNRSGGVTAQRQPNENGRPAGREFAI-PSLAHRFMAE
          AA.A..A.A.AA...S......P..QG..R.APV...GG..A..Q......P.G.E.A..PSLAH.F.AE
Retrocopy AAPASMALASAATTLSGES>QTPILQGLHRLAPVGMAGGAPALGQ*S*KTHPVGTEYAV>PSLAHGFKAE

Parental  MVDFFIL-FFIKATMVLTIMHVSGIKDISKFAMHYIIEEIDEDTSMEDLQKMMIVALIYRLLVCVYEIIC
          MV.FFIL..FIK.T.VLTIMHVS.IK.IS.FA..Y.IEE.DED.SM.D.QK..I.AL..RLLVCV.EIIC
Retrocopy MVHFFIL>TFIKVTVVLTIMHVSEIKNISEFAIYYMIEELDEDASMQDVQKIIIRALVFRLLVCVDEIIC

Parental  IWGAGGA-TPGKFLLGLRVVTCDTSVLIAPNRVLVIPSSNVNIFRSIIRALIKNFSIASFFPAFITLLFF
          I....GA.TPGKFLLGL.V.T.DTS..IAP..VLVI.SSNVNI..SII.A.....SIASF.P.FI.LL.F
Retrocopy ISEGSGA<TPGKFLLGLHVMTYDTSEFIAPSNVLVIHSSNVNITMSII*AYV---SIASFPPVFIRLLSF

Parental  QHNRTA
          QHN.TA
Retrocopy QHNQTA

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_1866 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1866 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137414	2 retrocopies	retro_hsap_2166, retro_hsap_4922,
Macaca mulatta	ENSMMUG00000001992	1 retrocopy	retro_mmul_904,
Monodelphis domestica	ENSMODG00000024641	1 retrocopy	retro_mdom_1866 ,
Nomascus leucogenys	ENSNLEG00000001130	2 retrocopies	retro_nleu_2828, retro_nleu_460,
Pan troglodytes	ENSPTRG00000017751	2 retrocopies	retro_ptro_1652, retro_ptro_3296,