RetrogeneDB ID: retro_mdom_1446

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:90574789..90575225(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPK
• Ensembl ID: ENSMODG00000019645
• Aliases: None
• Description: centromere protein K [Source:HGNC Symbol;Acc:29479]

Sequence

>retro_mdom_1446
CAAGAGCAACAGTGGTTGAATGAGCAAGAACAGCTAGTAATATTTCAGTGAAAAATGTAAGGAACGAAAAAATCAAGTGA
TACCATTTTCTGAGCAAAGGACTTTTTTTTAAAAATGAAAACTAAAATGACTAACATACAAAGGTATAGAGAGAAACTGT
TGACCTCTCTGGGTGAGTTTCTAGACAAGCATTTTCCTTTCCCTGAAAAAAAATGGAAATAAGAAGAGAAAAAGAGAGTG
TAAGCCAACTGCACAACTAAAGACATTGCATGAAATTTTAGAGGTTCATATAAATTGCTTACTTCAGAAGTCTCCACATG
ATCCATACATAAATGATTCCTTTTGGCCACCTTATATTGAGCTGCTGCTGCATAGAGGAATTGCAATTAGACATCAAGAT
GATCCAAACCAAATCTGATTAGAAGTGTTTCATCAG

Alignment

ORF - retro_mdom_1446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.86 %
• Parental protein coverage: 53.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  REQEWLNEQEHLVTSLSKKCKERKNQVIPFSEQRTFFEMNTKMTKIQSQREKLLNSLGEFLDKHFPPP-E
          .EQ.WLNEQE.LV....K.....K.....F........M.TKMT.IQ..REKLL.SLGEFLDKHFP.P..
Retrocopy QEQQWLNEQEQLVIFQ*KM*GTKKSSDTIF*AKDXXXKMKTKMTNIQRYREKLLTSLGEFLDKHFPFP>X

Parental  ENGN-KRKRECKPTAQLKTLREILEVLINSLL-RSPYNPYVKIDDSYWPPYIELLLRNGIALRHQDDPNQ
          ..GN.KRKRECKPTAQLKTL.EILEV.IN.LL..SP..PY..I.DS.WPPYIELLL..GIA.RHQDDPNQ
Retrocopy XXGNKKRKRECKPTAQLKTLHEILEVHINCLLQKSPHDPY--INDSFWPPYIELLLHRGIAIRHQDDPNQ

Parental  IRLEAFHQ
          I.LE.FHQ
Retrocopy I*LEVFHQ

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_1446 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1446 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013993	1 retrocopy	retro_chof_1252,
Dipodomys ordii	ENSDORG00000007357	1 retrocopy	retro_dord_787,
Equus caballus	ENSECAG00000019165	1 retrocopy	retro_ecab_181,
Erinaceus europaeus	ENSEEUG00000005831	1 retrocopy	retro_eeur_81,
Monodelphis domestica	ENSMODG00000019645	1 retrocopy	retro_mdom_1446 ,
Oryctolagus cuniculus	ENSOCUG00000011568	2 retrocopies	retro_ocun_1199, retro_ocun_74,
Tursiops truncatus	ENSTTRG00000006527	1 retrocopy	retro_ttru_1310,