RetrogeneDB ID: retro_mmus_464

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:83705272..83705716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Khdc1a
• Ensembl ID: ENSMUSG00000067750
• Aliases: Khdc1a, AU014713, C88118, Ndg1
• Description: KH domain containing 1A [Source:MGI Symbol;Acc:MGI:2676610]

Sequence

>retro_mmus_464
ATGAGTGACCCACACAGGAAGGGGTGGCAGAATATGCCTGACTACTTCCACAGCCCACTGTTTTTTACATGAAAGAGGAC
CAGGGAGAGTACATATTTGGCCCTGAGGACAAATACCTTCACTTCATGGAGGCCCACAGCAACATCCTCATTCAGCTGGA
GGGATGGTTCATACCCTCAGGCCAAACATGAGTCACTGTGGTGGGACCATCTAAGGCAAGGTGTGGGTAATCGGCATGGT
CAGAAAAGTGGGGAGTAAGAAAACTTTAGATCAGACAAAAGGCAAGATGATGCTACTGCATATTGAGAGACATCCTCTGA
TGGAGCAAGACCTGTAGCTTCATCCAGAATCAGGGAGCAGTCATTGATTTCCAGAATGAGTGATACAACTTCTGCAGAAG
TTCCTCATTACGTGAGATTTCCTTTGACAGTTGTTTGGGGTTTC

Alignment

ORF - retro_mmus_464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 89.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSDLRRKGWWNVPDYFHSPL-VFDMEEDKEDYIFGPHDEYLHTLEVHSNTLIQLERWFTPTGQTRVTVVG
          MSD..RKGW.N.PDYFHSPL.VF.M.ED...YIFGP.D.YLH..E.HSN.LIQLE.WF.P.GQT.VTVVG
Retrocopy MSDPHRKGWQNMPDYFHSPL<VFYMKEDQGEYIFGPEDKYLHFMEAHSNILIQLEGWFIPSGQT*VTVVG

Parental  PLKAR-LWVMDMIRKVGSKNNLDQIKGKMMLLQIRDHPLRDRDLELHPESGSS-LWITTMNDTTFVEVPH
          P.KAR..WV..M.RKVGSK..LDQ.KGKMMLL.I..HPL...DL.LHPESGSS...I..M.DTT..EVPH
Retrocopy PSKAR<VWVIGMVRKVGSKKTLDQTKGKMMLLHIERHPLMEQDL*LHPESGSS<SLISRMSDTTSAEVPH

Parental  FLRFPLTVAWLF
          ..RFPLTV.W.F
Retrocopy YVRFPLTVVWGF

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

RNA Polymerase II activity near the 5' end of retro_mmus_464 was not detected

EST

No EST(s) were mapped for retro_mmus_464 retrocopy.

TSS

No TSS is located nearby retro_mmus_464 retrocopy 5' end.

Lab

retro_mmus_464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_464 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000009236	4 retrocopies	retro_dord_249, retro_dord_47, retro_dord_607, retro_dord_82,
Microcebus murinus	ENSMICG00000006451	1 retrocopy	retro_mmur_647,
Macaca mulatta	ENSMMUG00000018573	1 retrocopy	retro_mmul_84,
Mus musculus	ENSMUSG00000067750	1 retrocopy	retro_mmus_464 ,
Oryctolagus cuniculus	ENSOCUG00000028154	1 retrocopy	retro_ocun_735,
Otolemur garnettii	ENSOGAG00000006102	1 retrocopy	retro_ogar_2275,