RetrogeneDB ID: retro_mdom_955

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:20081560..20082304(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021220
• Aliases: None
• Description: None

Sequence

>retro_mdom_955
AGTGCAGAAGAAAGTTCTCCAGGATTGGATGAAGAGTCACCTAGTCATGGAAGTTCTGTCAGCTTAGAAGGGTGGCATCA
TTTCTGCATCACCAGCCAAATCAGGAAGACAGCAAGAAAGCTGTCCTCCTGACCTCCAGCATCAAACCCTGATGCTGAGG
GTGTTTTTGCAGTGGTGCCAAGACTTGAAGGAGTGCTACTTGACCAAACATCTTTTATTCTGGTCCATTTGGTGGGCTTC
TTCCATAGCTGGCTTTAACCTAGTGGTAAACTATGTCCAGGTTCTATGGGATCACAAGGCACCGTCTCAGACTTTTCATG
TGTGTAATGGAGCAGTAGAAGCTGTGGCAACATTTGGAGGTGCTTTGGCAGCCTTTGCGGTGGGATATCTAAAATCAACT
GGGATCTTTGGGGAGAATTGGCTTTAGGAATCTTCTCAGTCCTCGATGCTGCTTCAGTATTCCTCATGCGTCTCACCAAC
AATATCTGGGTGTGTTATGCCGGCCTTTTGATTTTCAAATCAGGTTATATGCTTCTCATAACCATTGCAGTATTTCAGAT
TGCAGTAAACCTCAGCACGGAGCGCTCTGCCTTAGTGTTTGGAGTCAACACCTTTATGGCTTTGGTGATTCAGACCATAA
TAACATTTATCGTAGTTGATTCTAAAGGTCTGAGTCTGCCCGTTGATATTCAGTTCCTAATTTATGGAAGCTACTTTTTA
GTCATTGCTGGAATGTTCATAGTG

Alignment

ORF - retro_mdom_955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 50.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TAKESSPGSPDEESPSHGSSVSLEG-GIISESPTKSGIQQESCPPGLQHKNLMLRVFLQWCQDLKECYLT
          .A.ESSPG..DEESPSHGSSVSLEG.GIIS.SP.KSG.QQESCPP.LQH..LMLRVFLQWCQDLKECYLT
Retrocopy SAEESSPGL-DEESPSHGSSVSLEG>GIISASPAKSGRQQESCPPDLQHQTLMLRVFLQWCQDLKECYLT

Parental  KHLLFWSIWWASSTAGFNLVLNYVQVLWDHKAPSQNSQVYNGAVEAVATFGGALASLAVGYLK-INWDLW
          KHLLFWSIWWASS.AGFNLV.NYVQVLWDHKAPSQ...V.NGAVEAVATFGGALA..AVGYLK.INWDLW
Retrocopy KHLLFWSIWWASSIAGFNLVVNYVQVLWDHKAPSQTFHVCNGAVEAVATFGGALAAFAVGYLK<INWDLW

Parental  GELALGIFSVLDAASVLLMRFTSNIWVCYAGFLIFKSGYMLLITIAVFQIAVNLSMERYALVFGVNTFMA
          GELALGIFSVLDAASV.LMR.T.NIWVCYAG.LIFKSGYMLLITIAVFQIAVNLS.ER.ALVFGVNTFMA
Retrocopy GELALGIFSVLDAASVFLMRLTNNIWVCYAGLLIFKSGYMLLITIAVFQIAVNLSTERSALVFGVNTFMA

Parental  LVIQTIITFIVVDSKGLSLPVETQFLVYGSYFFVIAGIFIV
          LVIQTIITFIVVDSKGLSLPV..QFL.YGSYF.VIAG.FIV
Retrocopy LVIQTIITFIVVDSKGLSLPVDIQFLIYGSYFLVIAGMFIV

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_955 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_955 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000135917	1 retrocopy	retro_hsap_3732,
Gorilla gorilla	ENSGGOG00000004344	1 retrocopy	retro_ggor_2518,
Monodelphis domestica	ENSMODG00000021220	1 retrocopy	retro_mdom_955 ,
Mustela putorius furo	ENSMPUG00000001374	1 retrocopy	retro_mputfur_1211,
Nomascus leucogenys	ENSNLEG00000013501	1 retrocopy	retro_nleu_2561,
Pongo abelii	ENSPPYG00000013242	1 retrocopy	retro_pabe_3209,
Pan troglodytes	ENSPTRG00000028998	1 retrocopy	retro_ptro_2526,