RetrogeneDB ID: retro_mdom_1033

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:300254553..300255193(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCKDK
• Ensembl ID: ENSMODG00000001837
• Aliases: None
• Description: branched chain ketoacid dehydrogenase kinase [Source:HGNC Symbol;Acc:16902]

Sequence

>retro_mdom_1033
TCTTCCAGAAGCTGAATGTGTACATTGGGCACTCATCACCTGGCCCTGCATTAGGACAATTCTAACTTTGTAGGAGTCAT
CTATATTCAACCCCCCACAAAGATCATTGAAAAGTGGGTGGACTTTGTCAGGAGGTTGTGTGGTAATGCCCCTCAAGTTC
GAATTAATAGCCACATGGCTGCCCGCTTCCCCTTCATCCCAATGCCCCTGAACTATATTCTTCCTGAGCTACTGAAGAAT
GGTATGAGGGCCATGATGGAAAGCCATCTGAATATTCCATATAACATTCTGGATATCATCATCATTATTGCCAACAATGA
CATTGACCTCATAATCAGAATTTCACATCAGGGTTGGGGGCATCACCCACCACTATTTGGACAAAGTGATGGACTACTAC
TTCACCACTACTGAGGCCAGCATTCAGGATCCTCGAATCAACCCACTTTTTGGTCAAGTGGATAAAAACAGCAATGTCCA
GCCAGGACCTATACTTGGATTTGGTTTTGGGCTTCCTACATCCCAGACCTATGCAGAATACCTAGGTGGCTCTCTTTGGC
TCCAGTCCTTGCAAGGGATTGGCACAAACATCTACATAAGTCTTCATCACATAGGTTGCAAGGAGAAGAGCTTCCAGATC

Alignment

ORF - retro_mdom_1033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 53.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPF
          .SR.....L.THHLALH.D...FVG.I.....P.KIIEKWVDF.RRLC....GNAP.VRIN.H.AARFPF
Retrocopy SSRS*MCTLGTHHLALH*DNSNFVGVIYIQ-PPTKIIEKWVDFVRRLC----GNAPQVRINSHMAARFPF

Parental  IPMPLDYILPELLKNAMRRAGHEESQLDTPYNVPDIVITIANNDIDLIIRISDRG-GGIAHHHLDKVMDY
          IPMPL.YILPELLKN.MR.....ES.L..PYN..DI.I.IANNDIDLIIRIS..G.GGI.HH.LDKVMDY
Retrocopy IPMPLNYILPELLKNGMRAM--MESHLNIPYNILDIIIIIANNDIDLIIRISHQG>GGITHHYLDKVMDY

Parental  HFTTAEASTQDPRISPLFGHLDTNSNGQSGPMHGFGFGLPTSRAYAEYLGGSLRLQSLQGIGTDVYLRLR
          .FTT.EAS.QDPRI.PLFG..D.NSN.Q.GP..GFGFGLPTS..YAEYLGGSL.LQSLQGIGT..Y..L.
Retrocopy YFTTTEASIQDPRINPLFGQVDKNSNVQPGPILGFGFGLPTSQTYAEYLGGSLWLQSLQGIGTNIYISLH

Parental  HIDGKEESFRI
          HI..KE.SF.I
Retrocopy HIGCKEKSFQI

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_1033 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1033 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000014497	1 retrocopy	retro_etel_614,
Monodelphis domestica	ENSMODG00000001837	1 retrocopy	retro_mdom_1033 ,
Monodelphis domestica	ENSMODG00000009035	2 retrocopies	retro_mdom_107, retro_mdom_1447,
Rattus norvegicus	ENSRNOG00000019485	1 retrocopy	retro_rnor_2322,