RetrogeneDB ID: retro_mdom_1625

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:230959122..230959461(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM168B
• Ensembl ID: ENSMODG00000018633
• Aliases: None
• Description: family with sequence similarity 168, member B [Source:HGNC Symbol;Acc:27016]

Sequence

>retro_mdom_1625
CACACAGTGTCTTATTCACCCACCAGTGGGACAGTGCCACTTTATTCATCATCACCCAACCCTTATCAGGCTGCAGTGTA
CTCTATTCAAAGAGCCTAGCCACAGCAGAATCTAAAAGCAGAGCAAGGCACTTTCTATTATTCCCAGCCATTGTTTGCAG
CACCACCTCAAGGAATTCATCACACCACAGTTGTGCAAACAAATGGCCTGCCAGCAACTATGTACCCAGCTCCCATTGTC
CCTCCAAGAAGAAATGGCCTGACTATGGAAATGGTTTCTGGGACCACTATGGAAATGTCAACAGGTGCTTTGTTGACTAC
TCATTCCCCTAGCCCTGTA

Alignment

ORF - retro_mdom_1625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.45 %
• Parental protein coverage: 57.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YKVSCSPTSGAVPPYSSSPNPYQTAVYPVRSAYPQQNPYAQQGT-YYTQPLYAAPPHVIHHTTVVQPNGM
          ..VS.SPTSG.VP.YSSSPNPYQ.AVY....A.PQQN..A.QGT.YY.QPL.AAPP..IHHTTVVQ.NG.
Retrocopy HTVSYSPTSGTVPLYSSSPNPYQAAVYSIQRA*PQQNLKAEQGTFYYSQPLFAAPPQGIHHTTVVQTNGL

Parental  PATMYPAPIPPPRGNGVTMGMVAGTTMAMSAGTLLTTHSPTPV
          PATMYPAPI.PPR.NG.TM.MV.GTTM.MS.G.LLTTHSP.PV
Retrocopy PATMYPAPIVPPRRNGLTMEMVSGTTMEMSTGALLTTHSPSPV

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_1625 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1625 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004222	2 retrocopies	retro_cfam_1748, retro_cfam_344,
Choloepus hoffmanni	ENSCHOG00000009590	1 retrocopy	retro_chof_551,
Equus caballus	ENSECAG00000017018	1 retrocopy	retro_ecab_27,
Felis catus	ENSFCAG00000000303	1 retrocopy	retro_fcat_1218,
Monodelphis domestica	ENSMODG00000018633	1 retrocopy	retro_mdom_1625 ,
Mustela putorius furo	ENSMPUG00000011824	1 retrocopy	retro_mputfur_454,
Ictidomys tridecemlineatus	ENSSTOG00000000206	2 retrocopies	retro_itri_191, retro_itri_262,
Tupaia belangeri	ENSTBEG00000017162	1 retrocopy	retro_tbel_83,