RetrogeneDB ID: retro_mdom_163

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:174370860..174371493(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024541
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000004596
• Aliases: None
• Description: None

Sequence

>retro_mdom_163
ATGCCCGGCGTGAAGCTGACCACCCAGGCCTACTGCAAGATGGTGCTGCACGGGGCCAAATACCCCCATTGCGCCGTCAA
CGGACTTCTTGTAGCCGAGAAGCAGAAGCCCCGCAAAGAGCAGCCGTCGCATGGCGGCCTGAGCTCTCACCAGACCCTCT
TCGTGGACTGTATCCCCCTCTTCCATGGCACCCTGGCCCTGGCCCCCATGCTGGAAGTGGCCCTAACCTTGATTGATTCA
TGGTGCAAAGATAATAGCTATGTGATTGCTGGTTATTATCAAGCTAATGAACATATAAACGACGCCAGTCCAAATCAGGT
TGCTGAGAAGGTAGCTTCCAGAATCGCTGAGGGCTTCAGTGACACCGCACTCATCATGATAGACAACACAAAGTTTACAA
TGGAGTGCATAGAACCCACCATTCATGTGTATGAGCATCATGAAAACAAATGGAGGTGCAGAGATCCACACTATGACTAT
TGTGAAGACTGGCCAGAAGCCCAGAGAATCTCGGCATCTCTCTTGGACAGCAGGTCTTATGAAACCCTTGTGGATTTTGA
TAACCACCTGGACGACATCCGAAATGATTGGACAAATCCAGAGATCAATAAAGCTGTTCTACACCTATATTAA

Alignment

ORF - retro_mdom_163 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.09 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGVKLTTQAYCKMVLHGAKYPHCAVNGLLVAEKQKPRKEQPSHGGLSSHQTLFVDCIPLFHGTLALAPM
          MPGVKLTTQAYCKMVLHGAKYPHCAVNGLLVAEKQKPRKEQPSHGGLSSHQTLFVDCIPLFHGTLALAPM
Retrocopy MPGVKLTTQAYCKMVLHGAKYPHCAVNGLLVAEKQKPRKEQPSHGGLSSHQTLFVDCIPLFHGTLALAPM

Parental  LEVALTLIDSWCKDNSYVIAGYYQANERIKDASPNQVAEKVASRIAEGFNDTALIMVDNTKFTMECIEPT
          LEVALTLIDSWCKDNSYVIAGYYQANE.I.DASPNQVAEKVASRIAEGF.DTALIM.DNTKFTMECIEPT
Retrocopy LEVALTLIDSWCKDNSYVIAGYYQANEHINDASPNQVAEKVASRIAEGFSDTALIMIDNTKFTMECIEPT

Parental  IHVYEHHENKWRCRDPHYDYCEDWPEAQRISASLLDSRSYETLVDFDNHLDDIRNDWTNPEINKAVLHL
          IHVYEHHENKWRCRDPHYDYCEDWPEAQRISASLLDSRSYETLVDFDNHLDDIRNDWTNPEINKAVLHL
Retrocopy IHVYEHHENKWRCRDPHYDYCEDWPEAQRISASLLDSRSYETLVDFDNHLDDIRNDWTNPEINKAVLHL

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_163 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_163 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019922	1 retrocopy	retro_cfam_2117,
Callithrix jacchus	ENSCJAG00000017312	1 retrocopy	retro_cjac_675,
Erinaceus europaeus	ENSEEUG00000011856	1 retrocopy	retro_eeur_44,
Macropus eugenii	ENSMEUG00000009360	5 retrocopies	retro_meug_1050, retro_meug_1386, retro_meug_636, retro_meug_709, retro_meug_97,
Monodelphis domestica	ENSMODG00000004596	1 retrocopy	retro_mdom_163 ,
Otolemur garnettii	ENSOGAG00000010372	1 retrocopy	retro_ogar_2503,