RetrogeneDB ID: retro_mdom_1091

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:64332555..64332950(-)
• Located in intron of: ENSMODG00000003250

Retrocopy information

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

Parental gene information

• Parental gene symbol: CINP
• Ensembl ID: ENSMODG00000013323
• Aliases: None
• Description: cyclin-dependent kinase 2 interacting protein [Source:HGNC Symbol;Acc:23789]

Sequence

>retro_mdom_1091
ATATATCTAAAATACAATAAGGAGTTTAAGATTTTGTACAAGGAACTTCATGACACTTTAGGAAACTTTGCTATGGTATA
GGTGAAAATGGTTAAAGTGGAAAACTTAACAACCAACAAAGTAATTTGTAACTGAGAATAATTACCATATAGGAAATGGA
AATTATCAGACACCTCTTTTTCAGAGGTGGCCTACATCCTATTTCTATGAAATTTCTCATAAGTTTTTAGAAATGTACAA
GAAAGAAATACAATGCACCATGATCAAAGAATTCTTCAATACTACAAATCAGAATCTCATCTTAAGCGACTGATCTATGT
ACTTGTACCAGCCCTATATTAAGAACAAGTCTGACATGGGAAAGCATGATGACCAAAAATGGACATCAAGCAATA

Alignment

ORF - retro_mdom_1091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.88 %
• Parental protein coverage: 62.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VYPKYNEELEMLCKELHDTLENLAKIQMKMEKLTS--TTKGICNLE-NYHRGNANDQTPLFHTWPTTYFY
          .Y.KYN.E...L.KELHDTL.N.A....KM.K.....T.K.ICN.E.NYH.GN.N.QTPLF..WPT.YFY
Retrocopy IYLKYNKEFKILYKELHDTLGNFAMV*VKMVKVENLTTNKVICN*E>NYHIGNGNYQTPLFQRWPTSYFY

Parental  EVSHKLSEMYKKEILLKRTIVEELAHAANQDLILSYLSMWLYQPYVENSKLDV-ESMLLETGHRAL
          E.SHK..EMYKKEI....T...E.....NQ.LILS..SM.LYQPY..N.K.D..ESM....GH.A.
Retrocopy EISHKFLEMYKKEI--QCTMIKEFFNTTNQNLILSD*SMYLYQPYIKN-KSDM>ESMMTKNGHQAI

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	23.24 RPM
SRP007412_cerebellum	0.00 RPM	16.32 RPM
SRP007412_heart	0.00 RPM	25.72 RPM
SRP007412_kidney	0.00 RPM	36.87 RPM
SRP007412_liver	0.00 RPM	24.17 RPM
SRP007412_testis	0.00 RPM	45.57 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1091 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1091 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013323	1 retrocopy	retro_mdom_1091 ,
Oryctolagus cuniculus	ENSOCUG00000026866	1 retrocopy	retro_ocun_1274,
Otolemur garnettii	ENSOGAG00000009451	1 retrocopy	retro_ogar_321,
Sarcophilus harrisii	ENSSHAG00000007660	3 retrocopies	retro_shar_293, retro_shar_294, retro_shar_594,