RetrogeneDB ID: retro_mmus_2683

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:107478528..107479080(-)
• Located in intron of: ENSMUSG00000070632

Retrocopy information

• Ensembl ID: ENSMUSG00000089628
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lsm12
• Ensembl ID: ENSMUSG00000020922
• Aliases: None
• Description: LSM12 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1919592]

Sequence

>retro_mmus_2683
GGAAGCCAGGTGTCGTGCTGGACGTGCCAGGAGCAGCGGCTGCAAGGTGAGGTGGTAGCCTTCGACTACCAGTCCAAAAT
GCTGGCTCTAAAATGTCCCTCTTCCAGTGGAAAACCCAACCATGCAGACATCTTGCTTATAAACTTACAGTATGTTTCAG
AAGTGGAAATAATTAATGATCGAACAGAAACCCCTCCTCCCCTAGCTTCACTCAATGTTAGTAAGCTTGCCAGCAAAGCA
CGGACGGAAAAGGAGGAGAAGCTGAGCCAGGCCTATGCAATCAGCGCTGGTGTCTCCCTGGAGGGCCAACAGCTCTTCCA
GACCATTCACAAGACCATTAAAGACTGTCAATGGCAAGAAAAAAACATTGTAGTCATGGAAGAAGTTGTTATTACACCCC
CATATCAAGTGGAAAATTGTAAAGGCAAAGAGGGGAGTGCACTGAGCCATGTACGCAAAATAGTTGAAAAACAATTTAGA
GACGTGGAAAGCCAAAAGATACTACAGCGTTCACAAGCCCAACAACCACAGAAGGAGGCTGCTCTGTCATCC

Alignment

ORF - retro_mmus_2683 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.37 %
• Parental protein coverage: 94.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLAS
          GSQVSC.TCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLAS
Retrocopy GSQVSCWTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLAS

Parental  LNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENC
          LNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDC.WQEKNIVVMEEVVITPPYQVENC
Retrocopy LNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCQWQEKNIVVMEEVVITPPYQVENC

Parental  KGKEGSALSHVRKIVEKHFRDVESQKILQRSQAQQPQKEAALSS
          KGKEGSALSHVRKIVEK.FRDVESQKILQRSQAQQPQKEAALSS
Retrocopy KGKEGSALSHVRKIVEKQFRDVESQKILQRSQAQQPQKEAALSS

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	0.09 RPM	25.05 RPM
SRP007412_cerebellum	0.04 RPM	24.32 RPM
SRP007412_heart	0.00 RPM	25.62 RPM
SRP007412_kidney	0.02 RPM	25.33 RPM
SRP007412_liver	0.08 RPM	23.38 RPM
SRP007412_testis	0.18 RPM	51.09 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2683 was not detected

EST

No EST(s) were mapped for retro_mmus_2683 retrocopy.

TSS

No TSS is located nearby retro_mmus_2683 retrocopy 5' end.

Lab

retro_mmus_2683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2683 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843, retro_cfam_312,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683 ,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,