RetrogeneDB ID: retro_mdom_1859

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:120505041..120505397(+)
• Located in intron of: ENSMODG00000018456

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPH
• Ensembl ID: ENSMODG00000025601
• Aliases: None
• Description: centromere protein H [Source:HGNC Symbol;Acc:17268]

Sequence

>retro_mdom_1859
AGAATAAAGGGTCAGATTAGACAACAGCCCCTGGAATAAAAAGCAGAAATTGAAGCAAGTAAAGAGTCCTCCAGATGAAT
TCGCAGAAGGCTTACTTCAAATGATTAAAGATCTAGAAAAGAAGTTGGAAGGGGTGAAGATCAATGTTGAAATGAAAGCT
CTAGCTTCAAAAAGGGTCCAGATTGCATATGCCCTTCAGAAAAAAACTGGAATCAAAGGACAGTGAATCTCAATTCCTCC
TGGCAATTTTGAAGAACATTTTAACTTTTAATAGTTCAGTACTGAAAGCACAGCAGGAAACTCATGACCTGGAGGAGAAA
CTGCTTGAAGTTAAGAAAAAGAGATTAAGACTTAAG

Alignment

ORF - retro_mdom_1859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.05 %
• Parental protein coverage: 57.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RIKDQIKQQLLEYKA-KIEASKERLPEESTEEGLLQMTEELEKKLEGVKINVEMKTLALKRVQMANALQK
          RIK.QI.QQ.LE.KA.K....K...P.....EGLLQM...LEKKLEGVKINVEMK.LA.KRVQ.A.ALQK
Retrocopy RIKGQIRQQPLE*KA>KLKQVKS--PPDEFAEGLLQMIKDLEKKLEGVKINVEMKALASKRVQIAYALQK

Parental  K-LESKDSESQFLLAILKKILTLNSSILKAQQETHDLEEKLLEVKKKRLRLK
          K.LESKDSESQFLLAILK.ILT.NSS.LKAQQETHDLEEKLLEVKKKRLRLK
Retrocopy K>LESKDSESQFLLAILKNILTFNSSVLKAQQETHDLEEKLLEVKKKRLRLK

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_1859 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1859 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007717	1 retrocopy	retro_cfam_961,
Choloepus hoffmanni	ENSCHOG00000011338	2 retrocopies	retro_chof_1939, retro_chof_982,
Monodelphis domestica	ENSMODG00000025601	1 retrocopy	retro_mdom_1859 ,
Mustela putorius furo	ENSMPUG00000014646	1 retrocopy	retro_mputfur_240,
Sarcophilus harrisii	ENSSHAG00000007822	4 retrocopies	retro_shar_805, retro_shar_806, retro_shar_807, retro_shar_809,
Tupaia belangeri	ENSTBEG00000011867	2 retrocopies	retro_tbel_4318, retro_tbel_4535,
Tarsius syrichta	ENSTSYG00000002098	1 retrocopy	retro_tsyr_199,