RetrogeneDB ID: retro_mdom_54

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:206731784..206732882(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024776
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000006971
• Aliases: None
• Description: None

Sequence

>retro_mdom_54
ATGGCCGCGGCCGCGGAGCAGCCTAGACATATGAGCGGAGTGAAACGAAGAGGGAAGGCCCAGTATGTGCAAGCTAAGAG
AGCCCGGCGCGGGGATGGCGGCGGCGGCCCGAGGCAGCTGGAGCCTGGGCTTCAGGGCATTCTCATTACCTGCAACATGA
ATGAGCGCAAGTGTGTGGAGGAGGCCTACAGCCTCCTCAATGAGTACGGGGACGACCTATACGGGCCCGAGAAGTTTGTA
GACAAGGATAAGCAACCATCTGGAAGTGAGGAGGAAGAGGAAGATGATGCAGAAGCTGCCTTGAAGAAAGAAGTCAGTGA
GATTCAGGCATCTACAGAATTGAGATTAAGACGATTTCAGTCAGTGGAAAGTGGAGCAAATAACGTGGTCTTCATTAGAA
CACTTGGCATAGAACCTGAGAAACTTGTACATCACATCCTAAAGGATATGTACACAACCAAGAAGAAGAAAACACGGGTT
ATTCTGCGTATGTTGCCCGTATCTGGCACATGCAAAGCTTTCTTAGAAGATATGAAAAAATATGCTGAAACCTTCTTGGA
ACCTTGGTTTAAAGCACCAAATAAAGGGACATTCCAGATTATTTACAAAGCACGTAATAATAGTCACATGAGCAGAGAAG
AAGTTATTAAAGAACTAGCAGGAATAGTGGGCTGCCTCAATCCTGAAAATAAGGTAGATCTCAGTAATCCCCAGTATACC
ATTGTGGTGGAAATCATTAAGGCTGTCTGCTGTCTGAGTGTTGTCAAAGATTACATGCTGTTCAGAAAATATAACCTTCA
GGAAGTGGTCAAGAGTAACAGAGAGGGGTCTCAGCCAAACCCTGGTCAGGACTCACAAGTAAAAAACGGGAAAAGAGCAA
AATTGGAGTTGGAAAACACAGACAAGGAGAATCTCAAGTCAAATGAAAGTGACTCTGCAGAAGACAAAAAGAATCCCCAG
GTGGTAGTAGAAGGTAGCAAAGAGGAGGGGCTGCAGAGCCCACTTTCTGAGACCCAGATGGAAAGTGAGAAAGGAGCCAA
ATCTGAAAATGGAAGCCAAGTTTTAGAAGATTTTAAATCAAAAGAAAGTGACCCAGAC

Alignment

ORF - retro_mdom_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.45 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAEQPRHMSGVKRRGKAQYVQAKRARRGGGGGGPRQLEPGLQGILITCNMNERKCVEEAYSLLNEYG
          MAAAAEQPRHMSGVKRRGKAQYVQAKRARRG.GGGGPRQLEPGLQGILITCNMNERKCVEEAYSLLNEYG
Retrocopy MAAAAEQPRHMSGVKRRGKAQYVQAKRARRGDGGGGPRQLEPGLQGILITCNMNERKCVEEAYSLLNEYG

Parental  DDLYGPEKFVDKDKQPSGSEEEEEDDAEAALKKEVSEIQASTELRLRRFQSVESGANNVVFIRTLGIEPE
          DDLYGPEKFVDKDKQPSGSEEEEEDDAEAALKKEVSEIQASTELRLRRFQSVESGANNVVFIRTLGIEPE
Retrocopy DDLYGPEKFVDKDKQPSGSEEEEEDDAEAALKKEVSEIQASTELRLRRFQSVESGANNVVFIRTLGIEPE

Parental  KLVHHILKDMYTTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFLEPWFKAPNKGTFQIIYKARNNSHM
          KLVHHILKDMYTTKKKKTRVILRMLP.SGTCKAFLEDMKKYAETFLEPWFKAPNKGTFQIIYKARNNSHM
Retrocopy KLVHHILKDMYTTKKKKTRVILRMLPVSGTCKAFLEDMKKYAETFLEPWFKAPNKGTFQIIYKARNNSHM

Parental  SREEVIKELAGIVGCLNPENKVDLSNPQYTIVVEIIKAVCCLSVVKDYMLFRKYNLQEVVKSNREGSQPN
          SREEVIKELAGIVGCLNPENKVDLSNPQYTIVVEIIKAVCCLSVVKDYMLFRKYNLQEVVKSNREGSQPN
Retrocopy SREEVIKELAGIVGCLNPENKVDLSNPQYTIVVEIIKAVCCLSVVKDYMLFRKYNLQEVVKSNREGSQPN

Parental  PGQDSQVKNGKRAKLELENTDKENLKSNESDSAEDKKNPQVVVEGSKEEGLQSPLSETQMESEKGAKSEN
          PGQDSQVKNGKRAKLELENTDKENLKSNESDSAEDKKNPQVVVEGSKEEGLQSPLSETQMESEKGAKSEN
Retrocopy PGQDSQVKNGKRAKLELENTDKENLKSNESDSAEDKKNPQVVVEGSKEEGLQSPLSETQMESEKGAKSEN

Parental  GSQVLEDFKSKESDPD
          GSQVLEDFKSKESDPD
Retrocopy GSQVLEDFKSKESDPD

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_54 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_54 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009499	1 retrocopy	retro_cjac_915,
Cavia porcellus	ENSCPOG00000008919	1 retrocopy	retro_cpor_71,
Felis catus	ENSFCAG00000015158	1 retrocopy	retro_fcat_195,
Homo sapiens	ENSG00000066654	1 retrocopy	retro_hsap_2521,
Gorilla gorilla	ENSGGOG00000005231	1 retrocopy	retro_ggor_1573,
Macaca mulatta	ENSMMUG00000004225	1 retrocopy	retro_mmul_1599,
Monodelphis domestica	ENSMODG00000006971	1 retrocopy	retro_mdom_54 ,
Nomascus leucogenys	ENSNLEG00000012369	1 retrocopy	retro_nleu_1443,
Pan troglodytes	ENSPTRG00000007848	1 retrocopy	retro_ptro_1466,