RetrogeneDB ID: retro_mdom_450

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:605430058..605430586(+)
• Located in intron of: ENSMODG00000005428

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS29
• Ensembl ID: ENSMODG00000011577
• Aliases: None
• Description: vacuolar protein sorting 29 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14340]

Sequence

>retro_mdom_450
ATGTTGGTGTTAGTATTAGGAGACCTGCATATCCCCCACTGATGCAACAGTCTGCCAGCTAAATTCAAAAAACTGCTGGT
GCCTGGAAAAATCCAGCACATCCTCTGCACTGGAAATCTTTGCACCAAAGAAAGTTATGACTATCTCAAGACTCTAGCTG
GAGATGTCCACATTGTTAGAGGAGACTTTGATGAGAATCTGAATTATCCAGAAGAGAAGGTTGTGACTGTTGGGCAGTTC
AAAATTGGTTTGATCCACGGACATCAAGTCATTCCATGGGGCGATATGGCCAGCTTAGCATTGCTGCAAAGACAGTTTGA
TGTGGATATTCTCATTTCAGGACACACACACAAGGCCTCTGAACATGAAAATAAGTTCTACATTAATCCAGGATCTGCCA
CTGGAGCCTATAATGCTCTGGAAACAAACATCATTCCTTCATTTGTACTGATGGATATCCAAGCTTCTACAGTGTATCAG
CTAATTGGAGATGATGTGAAAGTAGAACGAATCGAATATAAAAAATCC

Alignment

ORF - retro_mdom_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYP
          MLVLVLGDLHIPH.CNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYP
Retrocopy MLVLVLGDLHIPH*CNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYP

Parental  EQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYN
          E.KVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHK..A.EHENKFYINPGSATGAYN
Retrocopy EEKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHK--ASEHENKFYINPGSATGAYN

Parental  ALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS
          ALETNIIPSFVLMDIQASTV....YQLIGDDVKVERIEYKKS
Retrocopy ALETNIIPSFVLMDIQASTV----YQLIGDDVKVERIEYKKS

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	2.26 RPM	0.00 RPM
SRP007412_cerebellum	3.59 RPM	0.00 RPM
SRP007412_heart	1.40 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_450 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_450 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001891	1 retrocopy	retro_acar_30,
Loxodonta africana	ENSLAFG00000006176	1 retrocopy	retro_lafr_1115,
Monodelphis domestica	ENSMODG00000011577	1 retrocopy	retro_mdom_450 ,
Procavia capensis	ENSPCAG00000012049	1 retrocopy	retro_pcap_158,