RetrogeneDB ID: retro_mmus_709

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:48595278..48595806(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082250
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hn1l
• Ensembl ID: ENSMUSG00000024165
• Aliases: Hn1l, 2810430B18Rik, AL022629, C16orf34, D17Ertd441e
• Description: hematological and neurological expressed 1-like [Source:MGI Symbol;Acc:MGI:1196260]

Sequence

>retro_mmus_709
CGGTCCATGAAGCCCCTGGGAGGAGAACCGAGCGATCTTTTTGGAAGTCCAGAAGAAGGTATTTCTTCAAGCATGCCTAA
TAGGATGGCATCTGTTATTTTCGGACCAACTGAAGAACCTAAAAACATACCCAGGAGGACAAATTCTTTAGGAGGAAAAG
GAAGTGGGATCTTCGTTGAATCAAATCCTGTGCAAACTCGACAACGTTTGAATCCACCCGGTGGGAAGACCAGTAACATA
TTTGGGTCCCCAGTCACTGCCACTGTGCCTCTGGCACACCCAAACAAGCCCAAGGATCATGTTTGGCTGTGTGAAGGTGA
AGACTCTAAGTCTGACCTGAAAGCTGCAACAGACTCCACACCCAGAGGAGAGCCGGGCGACAAAGGAAGCTCAAAAGAAG
TAGAGCATGCAAAGATACCAGAGCCCACACCTACAGTTGACACTCATGAGCCCAGACTGGGGCTACGACCTCGCTCCCAC
AACAAAGTCCTGAACCCACCAGGAGGCAAATCCAGCCTCTCCTTCTAT

Alignment

ORF - retro_mmus_709 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 92.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSMKPPGGESSDLFGSPEEGISSSKPNRMASNIFGPTEEPKNIPKRTNPPGGKGSGIFDESTPVQTRQRL
          RSMKP.GGE.SDLFGSPEEGISSS.PNRMAS.IFGPTEEPKNIP.RTN..GGKGSGIF.ES.PVQTRQRL
Retrocopy RSMKPLGGEPSDLFGSPEEGISSSMPNRMASVIFGPTEEPKNIPRRTNSLGGKGSGIFVESNPVQTRQRL

Parental  NPPGGKTSDIFGSPVTATAPLAHPNKPKDHVLLCEGEDSKSDLKAATDSTPRGEQSDKGSSKEVEHAKIP
          NPPGGKTS.IFGSPVTAT.PLAHPNKPKDHV.LCEGEDSKSDLKAATDSTPRGE..DKGSSKEVEHAKIP
Retrocopy NPPGGKTSNIFGSPVTATVPLAHPNKPKDHVWLCEGEDSKSDLKAATDSTPRGEPGDKGSSKEVEHAKIP

Parental  EPTPTVDSHEPRLGPRPRSHNKVLNPPGGKSSLSFY
          EPTPTVD.HEPRLG.RPRSHNKVLNPPGGKSSLSFY
Retrocopy EPTPTVDTHEPRLGLRPRSHNKVLNPPGGKSSLSFY

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	4.49 RPM
SRP007412_cerebellum	0.00 RPM	4.73 RPM
SRP007412_heart	0.00 RPM	5.32 RPM
SRP007412_kidney	0.00 RPM	24.00 RPM
SRP007412_liver	0.00 RPM	18.92 RPM
SRP007412_testis	0.09 RPM	5.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_709 was not detected

EST

No EST(s) were mapped for retro_mmus_709 retrocopy.

TSS

No TSS is located nearby retro_mmus_709 retrocopy 5' end.

Lab

retro_mmus_709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_709 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008232	1 retrocopy	retro_amel_1019,
Cavia porcellus	ENSCPOG00000005352	2 retrocopies	retro_cpor_749, retro_cpor_892,
Dipodomys ordii	ENSDORG00000007521	1 retrocopy	retro_dord_269,
Macropus eugenii	ENSMEUG00000008873	4 retrocopies	retro_meug_1471, retro_meug_1628, retro_meug_189, retro_meug_258,
Mus musculus	ENSMUSG00000024165	3 retrocopies	retro_mmus_1204, retro_mmus_655, retro_mmus_709 ,
Oryctolagus cuniculus	ENSOCUG00000015551	1 retrocopy	retro_ocun_275,
Pteropus vampyrus	ENSPVAG00000016673	1 retrocopy	retro_pvam_99,
Rattus norvegicus	ENSRNOG00000024661	2 retrocopies	retro_rnor_25, retro_rnor_560,
Sorex araneus	ENSSARG00000012440	1 retrocopy	retro_sara_335,
Sarcophilus harrisii	ENSSHAG00000012700	1 retrocopy	retro_shar_184,
Tursiops truncatus	ENSTTRG00000011377	1 retrocopy	retro_ttru_429,