RetrogeneDB ID: retro_mmus_2442

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:25867991..25868449(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084018
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hn1
• Ensembl ID: ENSMUSG00000020737
• Aliases: None
• Description: hematological and neurological expressed sequence 1 [Source:MGI Symbol;Acc:MGI:1096361]

Sequence

>retro_mmus_2442
ACCACTACCACCAACTTTAAGGGTGTGGACCATAACAGCAGGAACAGCTCCCGGGTTTTGCAGCCTCCAGGTGGTGGATC
AAATTTTTCACTAGGCTTTGATGAACCAACAGAACAGCGTGTGAGGAAGAACAAGATGGCTTCTAACATCTTTGGGACAC
CTGAAGAGAAACCCCCATCTTGGGCCAAGTCAGCAGATGCCAAATTTAGTGGTGGCAGGGAAGATTCATTGTTGCCTGGA
ACACAGAGAAGTAACTCTTCTGAAGCAACCTCTGGAGATTTCTTAGACCTCAAAGGAGAAGGTGATATGCATGAAAATGT
GGACACAGACTTCCAAGATAACCTGGTGAAGATGGAAGAGAAGCCGGTGCCCACTGCTCTTGTGCGCAGGCCAGTGGTAC
AGCCCCAGCGTCATCCAGGAGAAACCCGCCTTGCCGCAAGTCCAGCCTGGTCTTGGGT

Alignment

ORF - retro_mmus_2442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.12 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TTTTTFKGVDPNSRNSSRVLRPPGGGSNFSLGFDEPAEQPVRKNKMASNIFGTPEENPPSWAKSAGSKSS
          TTTT.FKGVD.NSRNSSRVL.PPGGGSNFSLGFDEP.EQ.VRKNKMASNIFGTPEE.PPSWAKSA..K.S
Retrocopy TTTTNFKGVDHNSRNSSRVLQPPGGGSNFSLGFDEPTEQRVRKNKMASNIFGTPEEKPPSWAKSADAKFS

Parental  GGREDSESPGTQRSNSSEASSGDFLDLKGEGDMHENVDTDFQANLAQMEEKPVPAAPVPSPV-APAPVPS
          GGREDS..PGTQRSNSSEA.SGDFLDLKGEGDMHENVDTDFQ.NL..MEEKPVP.A.V..PV...AP..S
Retrocopy GGREDSLLPGTQRSNSSEATSGDFLDLKGEGDMHENVDTDFQDNLVKMEEKPVPTALVRRPV<GTAPASS

Parental  RRNPPGGKSSLVLG
          RRNPP..KSSLVLG
Retrocopy RRNPPCRKSSLVLG

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	32.85 RPM
SRP007412_cerebellum	0.04 RPM	14.20 RPM
SRP007412_heart	0.03 RPM	30.85 RPM
SRP007412_kidney	0.02 RPM	26.83 RPM
SRP007412_liver	0.00 RPM	5.54 RPM
SRP007412_testis	0.05 RPM	184.97 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2442 was not detected

EST

No EST(s) were mapped for retro_mmus_2442 retrocopy.

TSS

No TSS is located nearby retro_mmus_2442 retrocopy 5' end.

Lab

retro_mmus_2442 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2442 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014553	1 retrocopy	retro_cjac_2715,
Echinops telfairi	ENSETEG00000013294	1 retrocopy	retro_etel_89,
Homo sapiens	ENSG00000189159	1 retrocopy	retro_hsap_2343,
Gorilla gorilla	ENSGGOG00000013996	1 retrocopy	retro_ggor_1780,
Mustela putorius furo	ENSMPUG00000013971	1 retrocopy	retro_mputfur_1200,
Mus musculus	ENSMUSG00000020737	6 retrocopies	retro_mmus_1096, retro_mmus_2442 , retro_mmus_2574, retro_mmus_3706, retro_mmus_864, retro_mmus_934,
Nomascus leucogenys	ENSNLEG00000000610	1 retrocopy	retro_nleu_348,
Oryctolagus cuniculus	ENSOCUG00000002950	2 retrocopies	retro_ocun_1647, retro_ocun_457,
Ochotona princeps	ENSOPRG00000010887	2 retrocopies	retro_opri_537, retro_opri_88,
Pan troglodytes	ENSPTRG00000024246	1 retrocopy	retro_ptro_1715,
Rattus norvegicus	ENSRNOG00000003661	2 retrocopies	retro_rnor_1794, retro_rnor_454,
Ictidomys tridecemlineatus	ENSSTOG00000015171	1 retrocopy	retro_itri_1449,