RetrogeneDB ID: retro_mdom_1960

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:34335841..34336141(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf70
• Ensembl ID: ENSMODG00000001268
• Aliases: None
• Description: chromosome 19 open reading frame 70 [Source:HGNC Symbol;Acc:33702]

Sequence

>retro_mdom_1960
GTAAAGGCCGCTTTAGCTGGTGGGTCTTATACGTCGTTCATGATCAAGGGCTGCCGGGCTCATGTTCCCAGGTTCAGGCT
GCCTTACAGAGGGCTGTGGCGTCACTCCCAGGCGCCTTTAGCCATTACTCAGCTTTGCCACAAAGCAGATGGGCTTCCCT
GTAGAGCTCGCATCCATTCCCCATTTCAACCTTTCTCTCCGAGACAGCTGGAAGTCGGGCATGAGCAGCACGATGTCCTC
ACTGCCTGCCACTCCCTCAACAATCCAGAGTAGAGCGGCGAGGGCTGGAACTGCCTGGAG

Alignment

ORF - retro_mdom_1960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 93.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKTGIAGGS-VYLVYDLGLLGSSSQGQAALRRAQESVPEALNRYSAL-FSKQTGIHIEQIPSVPHINISL
          VK...AGGS..Y.V.D.GL.GS.SQ.QAAL.RA..S.P.A...YSAL...KQ.G...E...S.PH.N.SL
Retrocopy VKAALAGGS<LYVVHDQGLPGSCSQVQAALQRAVASLPGAFSHYSAL<ATKQMGFPVE-LASIPHFNLSL

Parental  RDSWNSGINSLMSSLSAAPSAIQKY-SNEGWNYLK
          RDSW.SG..S.MSSL.A.PS.IQ...S.EGWN.L.
Retrocopy RDSWKSGMSSTMSSLPATPSTIQSR<SGEGWNCLE

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_1960 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1960 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018796	2 retrocopies	retro_cfam_1706, retro_cfam_756,
Callithrix jacchus	ENSCJAG00000017076	2 retrocopies	retro_cjac_2329, retro_cjac_735,
Felis catus	ENSFCAG00000011836	1 retrocopy	retro_fcat_287,
Loxodonta africana	ENSLAFG00000026050	1 retrocopy	retro_lafr_1241,
Macaca mulatta	ENSMMUG00000028920	1 retrocopy	retro_mmul_251,
Monodelphis domestica	ENSMODG00000001268	1 retrocopy	retro_mdom_1960 ,
Mustela putorius furo	ENSMPUG00000006136	2 retrocopies	retro_mputfur_1001, retro_mputfur_217,
Procavia capensis	ENSPCAG00000006583	1 retrocopy	retro_pcap_106,
Tupaia belangeri	ENSTBEG00000013386	1 retrocopy	retro_tbel_1443,