RetrogeneDB ID: retro_mdom_28

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:49061713..49062367(+)
• Located in intron of: ENSMODG00000000074

Retrocopy information

• Ensembl ID: ENSMODG00000000077
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002955
• Aliases: None
• Description: GrpE protein homolog [Source:UniProtKB/TrEMBL;Acc:F6PJU2]

Sequence

>retro_mdom_28
ATGGCGGCACAGTGCTCGGGTTTGGTGCGACGGACTCTCCCAGCCATAGCCCTCTCCCTCCGAACCTCTTCTAGACGGCT
CTGTACAGCAACAAAACAGAAAAATAATGGCCAGAACTTAGAAGAGGATTCTAGTCAAAATGAACAGAAGATAGACAGTA
CCTCTACAGAGAAGACATTAATTGAAGAAAAGGTCAAATTAGAAGAACAGCTGAAAGAAACTTTGGAGAAATATAAGCGA
GCCTTAGCAGATACAGAGAACTTGAGGCAACGGAGCCAAAAATTGGTAGAAGAGGCAAAATTATATGGTATTCAAGGTTT
CTGTAAGGATTTACTAGAAGTTGCTGACATTTTGGAAAAGGCTACAGAAAGTGTCCCAAAAGATGAAATAAAGGAAGAAA
ATCCTCATTTGAAGAACCTATATGAGGGTCTTGTTATGACTGAAGTCCAGATTCAAAAAGTGTTCAAAAAACATGGTTTG
CTCAAATTAAATCCTCTTGGTGACAAATTTGATCCCTATGAACATGAAGCTTTGTTCCATACTCCAATAGAGGGGAAGGA
GCCTGGCACTGTTGCACTAGTAAACAAAGTTGGGTATAAGCTACACGGGCGAACCTTGAGACCTGCTTTGGTGGGTGTTG
TTAAAGAACCGTAA

Alignment

ORF - retro_mdom_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAQCSGLVRRTLPAIALSLRTSSRRLCTATKQKNNGQNLEEDSSQNEQKIDSTATEKTLIEEKVKLEEQ
          MAAQCSGLVRRTLPAIALSLRTSSRRLCTATKQKNNGQNLEEDSSQNEQKIDST.TEKTLIEEKVKLEEQ
Retrocopy MAAQCSGLVRRTLPAIALSLRTSSRRLCTATKQKNNGQNLEEDSSQNEQKIDSTSTEKTLIEEKVKLEEQ

Parental  LKETLEKYKRALADTENLRQRSQKLVEEAKLYGIQGFCKDLLEVADILEKATESVPKDEIKEENPHLKNL
          LKETLEKYKRALADTENLRQRSQKLVEEAKLYGIQGFCKDLLEVADILEKATESVPKDEIKEENPHLKNL
Retrocopy LKETLEKYKRALADTENLRQRSQKLVEEAKLYGIQGFCKDLLEVADILEKATESVPKDEIKEENPHLKNL

Parental  YEGLVMTEVQIQKVFKKHGLLKLNPLGDKFDPYEHEALFHTPIEGKEPGTVALVNKVGYKLHGRTLRPAL
          YEGLVMTEVQIQKVFKKHGLLKLNPLGDKFDPYEHEALFHTPIEGKEPGTVALVNKVGYKLHGRTLRPAL
Retrocopy YEGLVMTEVQIQKVFKKHGLLKLNPLGDKFDPYEHEALFHTPIEGKEPGTVALVNKVGYKLHGRTLRPAL

Parental  VGVVKEP
          VGVVKEP
Retrocopy VGVVKEP

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_28 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_28 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014364	1 retrocopy	retro_cfam_1776,
Homo sapiens	ENSG00000109519	3 retrocopies	retro_hsap_3746, retro_hsap_3864, retro_hsap_3870,
Loxodonta africana	ENSLAFG00000002590	1 retrocopy	retro_lafr_535,
Monodelphis domestica	ENSMODG00000002955	1 retrocopy	retro_mdom_28 ,
Mustela putorius furo	ENSMPUG00000010471	1 retrocopy	retro_mputfur_32,
Nomascus leucogenys	ENSNLEG00000011822	1 retrocopy	retro_nleu_2642,
Otolemur garnettii	ENSOGAG00000032291	1 retrocopy	retro_ogar_1765,
Procavia capensis	ENSPCAG00000011314	1 retrocopy	retro_pcap_388,
Pongo abelii	ENSPPYG00000014573	1 retrocopy	retro_pabe_3235,
Pan troglodytes	ENSPTRG00000015894	3 retrocopies	retro_ptro_2544, retro_ptro_2633, retro_ptro_2636,
Sarcophilus harrisii	ENSSHAG00000007667	1 retrocopy	retro_shar_766,