RetrogeneDB ID: retro_mmus_3720

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:157016231..157017530(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000085711
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Suclg2
• Ensembl ID: ENSMUSG00000061838
• Aliases: Suclg2, AF171077, AW556404, D6Wsu120e, SCS-betaG
• Description: succinate-Coenzyme A ligase, GDP-forming, beta subunit [Source:MGI Symbol;Acc:MGI:1306824]

Sequence

>retro_mmus_3720
ATGGCGTCCCCGGTGGCCATCTCGGCGCAGGCTGGGAAGCTTCTGCGAGAGCGAGCGCTGGGGCCGCTCCTGGAGGTCAG
GTCCCAGGCAGGTCACTTAACCCCCCGAAGATGGCTGAACCTGCAGGAGTACCAGAGCAAGAAGCTCATGTCAGAGCACG
GAGTGAGAGTGCAGAGGTTCTTTGTTGCCAACACTGCTAAAGAGGCTCTGGAGGCAGCCAAGAGATTGAATGCAAAAGAA
ATTGTTTTAAAAGCCCAGATCTTAGCTGGAGGAAGAGGAAAAGGTGTCTTCAATAGCGGTTTGAAAGGAGGGGTTCATTT
AACAAAAGACCCTAAAGTAGTGGGAGAGTTGGCTCAACAGATGATTGGTTATAATCTAGCAACAAAACAAACTCCAAAAG
AAGGTGTGAAAGTTAACAAGGTGATGGTTGCTGAAGCCCTGGATATTTCTAGAGAAACGTACTTGGCCATTCTAATGGAC
CGGTCCCATAATGGCCCTGTGATAGTGGGAAGTCCTCAGGGGGGCGTTGATATTGAGGAAGTGGCAGTTTCCAGTCCAGA
ACTCATCTTTAAGGAGCAGATTGACATCTTTGAAGGGATAAAGGATAGCCAGGCCCAGCGCATGGCAGAAAATCTGGGCT
TCCTTGGGTCTCTGAAAAACCAGGCTGCAGATCAGATTAAAAAGCTGTACCATCTCTTCCTGAAGATTGATGCCACTCAG
GTGGAAGTGAACCCCTTCGGTGAAACTCCAGAAGGACAAGTTGTCTGTTTTGATGCCAAGATAAACTTTGATGACAATGC
TGAGTTCCGACAAAAGGACATATTTGCTATGGACGACAAATCCGAGAATGAGCCCATTGAAAATGAAGCTGCCAGATACG
ATCTCAAGTATATAGGACTGGACGGGAACATCACCTGCTTCGTGAATGGTGCTGGGCTGGCCATGGCTACCTGCGACATC
ATCTTCCTGAACGGAGGGAAGCCAGCGAACTTCTTGGACCTTGGAGGTGGTGTAAAGGAAGCCCAAGTCTATGAAGCATT
CAAACTGCTCACGTCTGACCCCAAGGTGGAAGCCATTCTCGTCAATATCTTTGGTGGGATTGTCAACTGTGCCATCATTG
CCAACGGAATCACCAAAGCCTGCCGGGAGCTGGAGCTCAAGGTGCCACTGGTAGTCCGGCTTGAAGGAACTAATGTGCAG
GAGGCTCAGAATATCTTCAAGAGCAGCGGACTCCCCATCACGTCAGCTGTGGACCTGGAGGATGCAGCCAAGAAAGCTGT
TGCCAGTGTGGCAAAGAAG

Alignment

ORF - retro_mmus_3720 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASPVAIAAQAGKLLRERALRPLLAVRSQAGHLTPRRWLNLQEYQSKKLMSEHGVRVQRFFVANTAKEAL
          MASPVAI.AQAGKLLRERAL.PLL.VRSQAGHLTPRRWLNLQEYQSKKLMSEHGVRVQRFFVANTAKEAL
Retrocopy MASPVAISAQAGKLLRERALGPLLEVRSQAGHLTPRRWLNLQEYQSKKLMSEHGVRVQRFFVANTAKEAL

Parental  EAAKRLNAKEIVLKAQILAGGRGKGVFNSGLKGGVHLTKDPKVVGELAQQMIGYNLATKQTPKEGVKVNK
          EAAKRLNAKEIVLKAQILAGGRGKGVFNSGLKGGVHLTKDPKVVGELAQQMIGYNLATKQTPKEGVKVNK
Retrocopy EAAKRLNAKEIVLKAQILAGGRGKGVFNSGLKGGVHLTKDPKVVGELAQQMIGYNLATKQTPKEGVKVNK

Parental  VMVAEALDISRETYLAILMDRSHNGPVIVGSPQGGVDIEEVAASSPELIFKEQIDIFEGIKDSQAQRMAE
          VMVAEALDISRETYLAILMDRSHNGPVIVGSPQGGVDIEEVA.SSPELIFKEQIDIFEGIKDSQAQRMAE
Retrocopy VMVAEALDISRETYLAILMDRSHNGPVIVGSPQGGVDIEEVAVSSPELIFKEQIDIFEGIKDSQAQRMAE

Parental  NLGFLGSLKNQAADQITKLYHLFLKIDATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDK
          NLGFLGSLKNQAADQI.KLYHLFLKIDATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDK
Retrocopy NLGFLGSLKNQAADQIKKLYHLFLKIDATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDK

Parental  SENEPIENEAARYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKEAQVYEAFKLL
          SENEPIENEAARYDLKYIGLDGNI.CFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKEAQVYEAFKLL
Retrocopy SENEPIENEAARYDLKYIGLDGNITCFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKEAQVYEAFKLL

Parental  TSDPKVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVVRLEGTNVQEAQNILKSSGLPITSAVDLE
          TSDPKVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVVRLEGTNVQEAQNI.KSSGLPITSAVDLE
Retrocopy TSDPKVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVVRLEGTNVQEAQNIFKSSGLPITSAVDLE

Parental  DAAKKAVASVAKK
          DAAKKAVASVAKK
Retrocopy DAAKKAVASVAKK

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	0.07 RPM	7.97 RPM
SRP007412_cerebellum	0.00 RPM	6.47 RPM
SRP007412_heart	0.25 RPM	70.79 RPM
SRP007412_kidney	1.39 RPM	139.85 RPM
SRP007412_liver	0.90 RPM	110.46 RPM
SRP007412_testis	0.00 RPM	5.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3720 was not detected

EST

No EST(s) were mapped for retro_mmus_3720 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_155999	395 libraries	210 libraries	404 libraries	38 libraries	25 libraries

The graphical summary, for retro_mmus_3720 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3720 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000172340	1 retrocopy	retro_hsap_1044,
Gorilla gorilla	ENSGGOG00000027438	1 retrocopy	retro_ggor_825,
Myotis lucifugus	ENSMLUG00000017294	1 retrocopy	retro_mluc_695,
Macaca mulatta	ENSMMUG00000009693	2 retrocopies	retro_mmul_1273, retro_mmul_1995,
Mus musculus	ENSMUSG00000061838	1 retrocopy	retro_mmus_3720 ,
Nomascus leucogenys	ENSNLEG00000007553	1 retrocopy	retro_nleu_915,
Otolemur garnettii	ENSOGAG00000006190	1 retrocopy	retro_ogar_161,
Pongo abelii	ENSPPYG00000013735	1 retrocopy	retro_pabe_2624,
Pteropus vampyrus	ENSPVAG00000004554	1 retrocopy	retro_pvam_912,