RetrogeneDB ID: retro_mdom_1086

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:41552288..41552748(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SC5D
• Ensembl ID: ENSMODG00000013028
• Aliases: None
• Description: sterol-C5-desaturase [Source:HGNC Symbol;Acc:10547]

Sequence

>retro_mdom_1086
GTTTCAATATTTCTGCCAAAGGTTCAAGTTTACAGCAAACTTTATGAATGCATAGAAGATTCATGATATGTTTGGGCTGA
AGTCATTCTTAATATGATATCCTTCCTCTTCTTTAATGATTTTCTTTAATATACTGGTTTCATCAAACTCTTCATAAACT
CTTATATAAGCAACTACATAAGTCTCATTATGTTTAGAACATTATTCATCCATTACAAGTCATGTTCACAGTGTATATGA
CTTCCTTCAAGTTCTACTATATCACAAATACTCTTTCCTCTTTCCATTACAAAAAGTAGTTTATATAGGTCTATACATTA
TTGTGAAAGTCTATGCAATTTCCACTCAGGATGGTGACTACTGAGTTCCAAGATTCTTAGAAGCAGTTATTAATTTCAGA
GCTTATCACACAAATCACCACCCTTATTTTGACTATAACTATGTTCAATATTTCATGCTG

Alignment

ORF - retro_mdom_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.14 %
• Parental protein coverage: 51.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAIFLAEIRGYSKLYDRIEDSPYGWLGVILSMASFLFFTD-MSIYWIHRGLHHKLVYKRLHKPHHVWKIT
          V.IFL.....YSKLY..IEDS.Y.W..VIL.M.SFLFF.D..S.........HKL.YK.LHK.H.V..I.
Retrocopy VSIFLPKVQVYSKLYECIEDS*YVWAEVILNMISFLFFND<FSLIYWFHQTLHKLLYKQLHKSHYV*NII

Parental  TP-FASHAFHPMDGFLQGVPYHIYPFFFPLHKVVYLALYIIVNLWTISIHDGYYQVPKILEPFINGAAHH
          .P...SH..H....FLQ...YH.Y.F.FPL.KVVY..LYIIV....IS..DG.Y.VP..LE..IN..A.H
Retrocopy HP<ITSHV-HSVYDFLQVLLYHKYSFLFPLQKVVYIGLYIIVKVYAISTQDGDY*VPRFLEAVINFRAYH

Parental  TDHHLFFDYNYGQYFTL
          T.HH..FDYNY.QYF.L
Retrocopy TNHHPYFDYNYVQYFML

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_1086 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1086 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019246	1 retrocopy	retro_btau_813,
Canis familiaris	ENSCAFG00000011805	1 retrocopy	retro_cfam_291,
Callithrix jacchus	ENSCJAG00000007436	1 retrocopy	retro_cjac_1911,
Monodelphis domestica	ENSMODG00000013028	1 retrocopy	retro_mdom_1086 ,
Mustela putorius furo	ENSMPUG00000005754	1 retrocopy	retro_mputfur_484,
Ochotona princeps	ENSOPRG00000003219	1 retrocopy	retro_opri_1143,
Ictidomys tridecemlineatus	ENSSTOG00000008946	1 retrocopy	retro_itri_964,
Tupaia belangeri	ENSTBEG00000000490	1 retrocopy	retro_tbel_4326,
Tarsius syrichta	ENSTSYG00000011139	1 retrocopy	retro_tsyr_1097,
Tursiops truncatus	ENSTTRG00000006908	1 retrocopy	retro_ttru_777,