RetrogeneDB ID: retro_mdom_1654

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:60589081..60589396(-)
• Located in intron of: ENSMODG00000007207

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOCS2
• Ensembl ID: ENSMODG00000019459
• Aliases: None
• Description: molybdenum cofactor synthesis 2 [Source:HGNC Symbol;Acc:7193]

Sequence

>retro_mdom_1654
GAAAAAGTTGTTAGCTTAGAATATGAAGACTATGTACCAATGGCAGAAGCTAAAGTTAGAAAAATATGTAATGCTGTTAG
ACAGCAGTGGCCAGTCAAGCACATAGCCATATGCCATCGGCTTGGCTTAGTTCCAGTAACAGAAGCAAGTGTGGTCATTG
CTGTGTCTTCAGCACACAGGGCTGCATCTCTTGAAGCTGTGAAATATATCATTGATATATTAAAGGCCAAAGTTCCAATT
TGGAAAAAGGAGCTCTATGAAGAAGAAACATCATCTTGGAAAAGAAATAAAGAATGCTTTTGGACAAAAAATAAT

Alignment

ORF - retro_mdom_1654 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 55.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKVVSLEYEAYVPMAEAEVRKICNAVRQQWPVKHIAICHRLGLVPVTEASVVIAVSSAHRAASLEAVKYI
          .KVVSLEYE.YVPMAEA.VRKICNAVRQQWPVKHIAICHRLGLVPVTEASVVIAVSSAHRAASLEAVKYI
Retrocopy EKVVSLEYEDYVPMAEAKVRKICNAVRQQWPVKHIAICHRLGLVPVTEASVVIAVSSAHRAASLEAVKYI

Parental  IDTLKAKVPIWKKELYEEETSSWKRNKECFWTKND
          ID.LKAKVPIWKKELYEEETSSWKRNKECFWTKN.
Retrocopy IDILKAKVPIWKKELYEEETSSWKRNKECFWTKNN

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_1654 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1654 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005380	1 retrocopy	retro_btau_487,
Cavia porcellus	ENSCPOG00000015752	2 retrocopies	retro_cpor_746, retro_cpor_748,
Macaca mulatta	ENSMMUG00000020449	1 retrocopy	retro_mmul_581,
Monodelphis domestica	ENSMODG00000019459	1 retrocopy	retro_mdom_1654 ,
Oryctolagus cuniculus	ENSOCUG00000011406	1 retrocopy	retro_ocun_575,
Otolemur garnettii	ENSOGAG00000011108	1 retrocopy	retro_ogar_2170,
Pteropus vampyrus	ENSPVAG00000010175	1 retrocopy	retro_pvam_633,
Ictidomys tridecemlineatus	ENSSTOG00000010607	1 retrocopy	retro_itri_241,
Tupaia belangeri	ENSTBEG00000008942	3 retrocopies	retro_tbel_1128, retro_tbel_216, retro_tbel_3310,
Tarsius syrichta	ENSTSYG00000001351	1 retrocopy	retro_tsyr_510,