RetrogeneDB ID: retro_mmus_3722

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:157650709..157651299(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081505
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: l7Rn6
• Ensembl ID: ENSMUSG00000062797
• Aliases: None
• Description: lethal, Chr 7, Rinchik 6 [Source:MGI Symbol;Acc:MGI:96738]

Sequence

>retro_mmus_3722
ATGTTTGGCTGCCTGGTGGTGGGGAGGCTGGTGCAAACAGCTGCACAGCAAGTGGCAGAGGATAAATTTGTTTTTTGACT
TGCCCGATTATGAAAATATCAACCATGTTGTGGTTTTTATGCTGGGAACAATCCCATTTCCTGAGGGGATGGGAGGATCT
GTCTACTTTTCCTATCCTGATTCAAATGGAGTGCCAATGTGGCAGCTCCTAGGATTTGTCACGAATGGGAAGCCAAGTGC
CATCTTCAAAATATCAGGTCTTAAACCTACAGAAGAAAGCCAGCACCCATTTGGAGCCATGAATATTGTGCAAACCCCAT
CTGTTGCCCGGATTGGAATCTCGGTGGAATCGTTGGACAGTCTGGCTCAGCAGACTCCTGTAAGGCAGTGCTGCTATGCC
CTCGGTTGACTCCTCTATGCAGTTCACACAGAAGATGTTGGACAACTTCTACAATTTTGCTTCATTGTTTCTTCTCTCTC
AGATCCAGATGACACCAAACCCATCAGAAATGTTCATCCCAGCAAACGCGGCTCTGAAATGGTATGAAAACTTTCAAAGA
CAACTAGCACAAAACCCTCTCTTTTGGAAA

Alignment

ORF - retro_mmus_3722 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.9 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFGCLVAGRLVQTAAQQVAEDKFV-FDLPDYENINHVVVFMLGTIPFPEGMGGSVYFSYPDSNGVPVWQL
          MFGCLV.GRLVQTAAQQVAEDKFV.FDLPDYENINHVVVFMLGTIPFPEGMGGSVYFSYPDSNGVP.WQL
Retrocopy MFGCLVVGRLVQTAAQQVAEDKFV>FDLPDYENINHVVVFMLGTIPFPEGMGGSVYFSYPDSNGVPMWQL

Parental  LGFVTNGKPSAIFKISGLKSGEGSQHPFGAMNIVRTPSVAQIGISVELLDSLAQQTPV-GSAAVSSVDSF
          LGFVTNGKPSAIFKISGLK..E.SQHPFGAMNIV.TPSVA.IGISVE.LDSLAQQTPV.GSAA..SVDS.
Retrocopy LGFVTNGKPSAIFKISGLKPTEESQHPFGAMNIVQTPSVARIGISVESLDSLAQQTPV>GSAAMPSVDSS

Parental  TQFTQKMLDNFYNFASSFALSQAQMTPNPSEMFIPANVVLKWYENFQRRLAQNPLFWK
          .QFTQKMLDNFYNFAS.F.LSQ.QMTPNPSEMFIPAN..LKWYENFQR.LAQNPLFWK
Retrocopy MQFTQKMLDNFYNFASLFLLSQIQMTPNPSEMFIPANAALKWYENFQRQLAQNPLFWK

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	20.70 RPM
SRP007412_cerebellum	0.00 RPM	15.81 RPM
SRP007412_heart	0.00 RPM	12.30 RPM
SRP007412_kidney	0.00 RPM	15.17 RPM
SRP007412_liver	0.03 RPM	10.24 RPM
SRP007412_testis	0.73 RPM	4.39 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3722 was not detected

EST

No EST(s) were mapped for retro_mmus_3722 retrocopy.

TSS

No TSS is located nearby retro_mmus_3722 retrocopy 5' end.

Lab

retro_mmus_3722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3722 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015605	1 retrocopy	retro_ecab_720,
Homo sapiens	ENSG00000149196	1 retrocopy	retro_hsap_4658,
Gorilla gorilla	ENSGGOG00000023168	1 retrocopy	retro_ggor_2891,
Myotis lucifugus	ENSMLUG00000016260	1 retrocopy	retro_mluc_784,
Mus musculus	ENSMUSG00000062797	1 retrocopy	retro_mmus_3722 ,
Nomascus leucogenys	ENSNLEG00000016224	1 retrocopy	retro_nleu_1095,
Oryctolagus cuniculus	ENSOCUG00000013108	2 retrocopies	retro_ocun_1147, retro_ocun_280,
Pongo abelii	ENSPPYG00000003746	1 retrocopy	retro_pabe_3618,
Pan troglodytes	ENSPTRG00000004144	1 retrocopy	retro_ptro_3094,
Tupaia belangeri	ENSTBEG00000009192	2 retrocopies	retro_tbel_1594, retro_tbel_3248,
Tursiops truncatus	ENSTTRG00000012267	1 retrocopy	retro_ttru_562,