RetrogeneDB ID: retro_mmus_834

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:107004069..107004576(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083356
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Memo1
• Ensembl ID: ENSMUSG00000058704
• Aliases: Memo1, 0610016J10Rik, D930048L02Rik
• Description: mediator of cell motility 1 [Source:MGI Symbol;Acc:MGI:1924140]

Sequence

>retro_mmus_834
TGGGTCCTTGGGCCTTCCCATCATGTGCCCCTGTCTCGATGTACACGCTCCAGTGTACATATATATAGGACTCCTCTGTA
TGACCTTCATATTGACCAAAAGATTTACAGAGAGCTACGGAAGACAGGAATGTTTGAACGCATGTCTGTGCAGACAGATG
AAGTCCAACACAGTATTGAAATGCATTTGCCTTATACAGATAAAGCCATGGAAAGCCATAAAGATGAATTAGCCATTATT
CCCGAACTGGTTGGAGCTCTGAGTGAGTCAAAAGAACAGGAATTTGGAAATCTCTTCAGTAAATATCTAGCGGATCCTAA
TAATCTCTGTGTGGTTTCTTCTGATTTCTGCCACTGGGGTCATAGGTCCCGTTACAGTTACTATGACAAATCCCAGGGGG
ACATTTACAGATCCATTGAACATCTAGATAAAATGGGTATGAGTATTATAGAACAATTAGATCCTGTAACTTTTAGCAAT
TATTTGAAGAAATACCGTAATACTCTG

Alignment

ORF - retro_mmus_834 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.21 %
• Parental protein coverage: 56.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FILGPSHHVPLSRCALSSVDIYRTPLYDLRIDQKIYGELWKTGMFERMSLQTDEDEHSIEMHLPYTAKAM
          ..LGPSHHVPLSRC..SSV.IYRTPLYDL.IDQKIY.EL.KTGMFERMS.QTDE..HSIEMHLPYT.KAM
Retrocopy WVLGPSHHVPLSRCTRSSVHIYRTPLYDLHIDQKIYRELRKTGMFERMSVQTDEVQHSIEMHLPYTDKAM

Parental  ESHKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSSDFCHWGQRFRYSYYDESQGEIYRSIE
          ESHKDE..IIP.LVGALSESKEQEFG.LFSKYLADP.NL.VVSSDFCHWG.R.RYSYYD.SQG.IYRSIE
Retrocopy ESHKDELAIIPELVGALSESKEQEFGNLFSKYLADPNNLCVVSSDFCHWGHRSRYSYYDKSQGDIYRSIE

Parental  HLDKMGMSIIEQLDPVSFSNYLKKYHNTI
          HLDKMGMSIIEQLDPV.FSNYLKKY.NT.
Retrocopy HLDKMGMSIIEQLDPVTFSNYLKKYRNTL

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	15.26 RPM
SRP007412_cerebellum	0.00 RPM	7.90 RPM
SRP007412_heart	0.00 RPM	23.01 RPM
SRP007412_kidney	0.00 RPM	17.42 RPM
SRP007412_liver	0.03 RPM	14.66 RPM
SRP007412_testis	0.05 RPM	49.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_834 was not detected

EST

No EST(s) were mapped for retro_mmus_834 retrocopy.

TSS

No TSS is located nearby retro_mmus_834 retrocopy 5' end.

Lab

retro_mmus_834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_834 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007771	1 retrocopy	retro_amel_1500,
Equus caballus	ENSECAG00000019946	1 retrocopy	retro_ecab_401,
Echinops telfairi	ENSETEG00000007994	1 retrocopy	retro_etel_561,
Felis catus	ENSFCAG00000001385	1 retrocopy	retro_fcat_642,
Homo sapiens	ENSG00000162959	2 retrocopies	retro_hsap_2507, retro_hsap_3522,
Myotis lucifugus	ENSMLUG00000016108	1 retrocopy	retro_mluc_1923,
Mus musculus	ENSMUSG00000058704	1 retrocopy	retro_mmus_834 ,
Nomascus leucogenys	ENSNLEG00000015577	1 retrocopy	retro_nleu_488,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Otolemur garnettii	ENSOGAG00000010975	3 retrocopies	retro_ogar_1860, retro_ogar_2049, retro_ogar_3050,
Pongo abelii	ENSPPYG00000012511	1 retrocopy	retro_pabe_2910,