RetrogeneDB ID: retro_mmus_2927

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:42951744..42952204(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080892
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam96b
• Ensembl ID: ENSMUSG00000031879
• Aliases: Fam96b, 1110019N10Rik
• Description: family with sequence similarity 96, member B [Source:MGI Symbol;Acc:MGI:1915773]

Sequence

>retro_mmus_2927
GGCAGCGGGCTACTAGAGAACGCTAACCCCCTCATCTATGAGCGTTCTGGGGAGTGGCCAGTGTGTCAGGCAAGGAAGAT
TAGGATGTGCCCGACAGCATCGAGGCTAGGGAGATCTTCGATCTTATCTGCTCCATTAATGACCGGGAGCATCCACTGAC
ACTGGAGGAATTGAACGTGGTAGAGCAAGTTCGGATTCAGGTTAGCAACCCAGAGAGCACAGTGGCCTTCACACCCACCA
TCCCACACTGCAACATGGCCACTCTTATTGGCCTCTCCATCAAAGTCAAGCTGCTGCAATCCCTTCCCCAGCGTTCAAGA
TTGATGTACACATTACACCCGGGACCCATGCTGCGGAGCATGCACTGAACAAACAACTTGCAGATAAGGAGCCAGTGGCA
GCTGCCCTGGAGAATATGCACCTGCTAGAGGTTGTTAATCAGTGTCTGTCCTCCTGCTCG

Alignment

ORF - retro_mmus_2927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.81 %
• Parental protein coverage: 95.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGGLLENANPLIYERSGERPV-TAGEEDEEVPDSIDAREIFDLIRSINDPEHPLTLEELNVVEQVRIQVS
          G.GLLENANPLIYERSGE.PV...G.ED..VPDSI.AREIFDLI.SIND.EHPLTLEELNVVEQVRIQVS
Retrocopy GSGLLENANPLIYERSGEWPV<VSGKED*DVPDSIEAREIFDLICSINDREHPLTLEELNVVEQVRIQVS

Parental  DPESTVAVAFTPTIPHCSMATLIGLSIKVKLLRSLPQR-FKMDVHITPGTHASEHAVNKQLADKERVAAA
          .PEST..VAFTPTIPHC.MATLIGLSIKVKLL.SLPQR.FK.DVHITPGTHA.EHA.NKQLADKE.VAAA
Retrocopy NPEST--VAFTPTIPHCNMATLIGLSIKVKLLQSLPQR<FKIDVHITPGTHAAEHALNKQLADKEPVAAA

Parental  LENTHLLEVVNQCLSARS
          LEN.HLLEVVNQCLS..S
Retrocopy LENMHLLEVVNQCLSSCS

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	11.14 RPM
SRP007412_cerebellum	0.00 RPM	20.71 RPM
SRP007412_heart	0.03 RPM	35.58 RPM
SRP007412_kidney	0.02 RPM	29.91 RPM
SRP007412_liver	0.00 RPM	12.78 RPM
SRP007412_testis	0.00 RPM	27.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2927 was not detected

EST

No EST(s) were mapped for retro_mmus_2927 retrocopy.

TSS

No TSS is located nearby retro_mmus_2927 retrocopy 5' end.

Lab

retro_mmus_2927 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2927 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017164	1 retrocopy	retro_amel_1340,
Bos taurus	ENSBTAG00000013931	1 retrocopy	retro_btau_609,
Canis familiaris	ENSCAFG00000020394	2 retrocopies	retro_cfam_479, retro_cfam_802,
Felis catus	ENSFCAG00000029216	2 retrocopies	retro_fcat_1464, retro_fcat_697,
Mustela putorius furo	ENSMPUG00000005303	2 retrocopies	retro_mputfur_1547, retro_mputfur_302,
Mus musculus	ENSMUSG00000031879	1 retrocopy	retro_mmus_2927 ,
Mus musculus	ENSMUSG00000032381	1 retrocopy	retro_mmus_1919,
Sarcophilus harrisii	ENSSHAG00000004698	1 retrocopy	retro_shar_590,
Tarsius syrichta	ENSTSYG00000005006	2 retrocopies	retro_tsyr_1305, retro_tsyr_149,