RetrogeneDB ID: retro_mdom_1369

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:168525112..168525444(-)
• Located in intron of: ENSMODG00000005699

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBD2
• Ensembl ID: ENSMODG00000014351
• Aliases: None
• Description: pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2 [Source:HGNC Symbol;Acc:24474]

Sequence

>retro_mdom_1369
GGCGAGCTTCTCCTCGAGCTCCCTGGGTTGCTTTGGGGTGCTCCAGGGGGCTGCCAGAGCCTGTAGGTCAAATATTCAGA
CTCTCATTGGCTAGCGTCAGAAGAAAGGAACCAGGCTATACATGATGACCTCAAAGCCTCAGGAGGGTACAAATTAATGA
AAAAGATGCTCTGTAAAAATAATTATTTCAAAATTGTTAATCAGGCTTTGTAATTTGTGTCCCATGTTGTGCTACAAACA
GAAAGATGAATCACCAAACTGAATACTTTAATATGTATAATGAGGTCCAGGTGACTCTTATTGCACATGACTGTAATGGA
CTGACCAAGAGA

Alignment

ORF - retro_mdom_1369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.26 %
• Parental protein coverage: 78.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GRLIPALLGSPWVAPGKSRSLSVMSAESHWLTTEERNQVIH-DLKASGWSEL-NERDAIYKEFCFKN-FN
          G.L...L.G..W.APG...SL.V....SHWL..EERNQ.IH.DLKASG...L.NE.DA..K...F.N..N
Retrocopy GELLLELPGLLWGAPGGCQSL*VKYSDSHWLASEERNQAIHDDLKASGGYKL<NEKDAL*K*L-FQN>VN

Parental  QAFGFMSRVALQAE-KMNHHPEWFNVYNKVQITLISHDCGGLTKR
          QA..F.S.V.LQ.E.KMNH..E.FN.YN.VQ.TLI.HDC.GLTKR
Retrocopy QAL*FVSHVVLQTE<KMNHQTEYFNMYNEVQVTLIAHDCNGLTKR

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	40.65 RPM
SRP007412_cerebellum	0.00 RPM	25.14 RPM
SRP007412_heart	0.00 RPM	99.68 RPM
SRP007412_kidney	0.00 RPM	55.31 RPM
SRP007412_liver	0.00 RPM	58.91 RPM
SRP007412_testis	0.00 RPM	13.16 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1369 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1369 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000019125	2 retrocopies	retro_dnov_645, retro_dnov_660,
Equus caballus	ENSECAG00000015810	2 retrocopies	retro_ecab_489, retro_ecab_871,
Erinaceus europaeus	ENSEEUG00000007051	1 retrocopy	retro_eeur_190,
Echinops telfairi	ENSETEG00000016658	2 retrocopies	retro_etel_1252, retro_etel_75,
Macropus eugenii	ENSMEUG00000003784	1 retrocopy	retro_meug_1185,
Myotis lucifugus	ENSMLUG00000012638	1 retrocopy	retro_mluc_1445,
Monodelphis domestica	ENSMODG00000014351	1 retrocopy	retro_mdom_1369 ,
Pteropus vampyrus	ENSPVAG00000000384	2 retrocopies	retro_pvam_63, retro_pvam_750,
Tursiops truncatus	ENSTTRG00000016874	3 retrocopies	retro_ttru_1135, retro_ttru_359, retro_ttru_511,