RetrogeneDB ID: retro_mmus_641

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:44169599..44170302(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ccdc137
• Ensembl ID: ENSMUSG00000049957
• Aliases: Ccdc137, 3110023B02Rik
• Description: coiled-coil domain containing 137 [Source:MGI Symbol;Acc:MGI:1914541]

Sequence

>retro_mmus_641
GGACAGCAGCGCAAAGAAAAGAAGAAAGTGAATTGCAAGCCTAAGAACCAGAATGAGCAAGAAATCCCTTTTCGGCTCTG
AGAGATTATGAGGAGCCGACAGGAGAGGAAAAAGACGCTAAGTAACAAGAAGAGGAAAAAAGGAGGCCCAGGTGGCTTTC
AAGAAGACATTGGAAAAGGAAGTGAAGGGGGAGGAGCCAGACATCGCTGTCCCCAAGTTCAAGCAAAGGAAGGGGGAGTC
TGATGTGGCCTACGTCCCGTGCATGGAGCAGGAGGCCCAACACGTACTGTTTCTTAGCAAGAACCAGGCCCCTCGGCAGC
CAGAGGTGCAGTCAGCTCCCAAGAAGTCTGAGAGGAAGAAAGCGTTCCAGAAGCGACGACTGGAAAAGGCCCAGAGAAAA
AGGGAAGCAAGAGCCGTGGACAGATTGGAGCAGGAGCTACTGAAAGATACTGTGAAGTTTGGAGAAGTTGTGTTGCAGCC
CCCAGAGCTGACAGTTCAGCCGAGGAGGAGCACAAGCAGAGATGCTCCTGGCAAGAAATCACTAATGCTGAAGAAGATGC
TGTTGGGTCCTGGTGGCGGGTCCCCGGCTCTAGCCACCTCACTGGCCCGCCAGCAGATCCTGGGGGAAGAGCGGGAACGG
GCTGTGTAGGCTTACAGAGCCCTGAAGAAGCTGCTTCGACAGGAAATGACACCTGCACAGCCA

Alignment

ORF - retro_mmus_641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.25 %
• Parental protein coverage: 81.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GQRSKEKKKVNCKPKNQDEQEIPFRLREIMRSRQEMKKTLSNKKRKK-EAQVAFKKTLEKEAKGEEPDIA
          GQ..KEKKKVNCKPKNQ.EQEIPFRL.EIMRSRQE.KKTLSNKKRKK.EAQVAFKKTLEKE.KGEEPDIA
Retrocopy GQQRKEKKKVNCKPKNQNEQEIPFRL*EIMRSRQERKKTLSNKKRKK>EAQVAFKKTLEKEVKGEEPDIA

Parental  VPKFKQRKGESDVAYVQRMEQEAQHVLFLSKNQAPRQPEVQAAPKKEKSERKKAFQKRRLEKAQRKREAR
          VPKFKQRKGESDVAYV..MEQEAQHVLFLSKNQAPRQPEVQ.APK..KSERKKAFQKRRLEKAQRKREAR
Retrocopy VPKFKQRKGESDVAYVPCMEQEAQHVLFLSKNQAPRQPEVQSAPK--KSERKKAFQKRRLEKAQRKREAR

Parental  AVDRLEQELLKDTVKFGEVVLQPPELTVQPRRSTSRDAPGKKSLMLKKMLLGPGGGSPAPATSLARQRIL
          AVDRLEQELLKDTVKFGEVVLQPPELTVQPRRSTSRDAPGKKSLMLKKMLLGPGGGSPA.ATSLARQ.IL
Retrocopy AVDRLEQELLKDTVKFGEVVLQPPELTVQPRRSTSRDAPGKKSLMLKKMLLGPGGGSPALATSLARQQIL

Parental  GEERERAVQAYRALKKLHRQEMTPAQP
          GEERERAV.AYRALKKL.RQEMTPAQP
Retrocopy GEERERAV*AYRALKKLLRQEMTPAQP

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	20.79 RPM
SRP007412_cerebellum	0.00 RPM	19.32 RPM
SRP007412_heart	0.00 RPM	6.69 RPM
SRP007412_kidney	0.00 RPM	14.96 RPM
SRP007412_liver	0.00 RPM	9.86 RPM
SRP007412_testis	6.22 RPM	7.91 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_641 was not detected

EST

No EST(s) were mapped for retro_mmus_641 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_3458	1064 libraries	5 libraries	0 libraries	1 library	2 libraries

The graphical summary, for retro_mmus_641 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_641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_641 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014878	1 retrocopy	retro_eeur_523,
Homo sapiens	ENSG00000185298	1 retrocopy	retro_hsap_2661,
Gorilla gorilla	ENSGGOG00000009333	1 retrocopy	retro_ggor_1857,
Macaca mulatta	ENSMMUG00000008831	1 retrocopy	retro_mmul_1511,
Monodelphis domestica	ENSMODG00000002713	1 retrocopy	retro_mdom_1355,
Mus musculus	ENSMUSG00000049957	1 retrocopy	retro_mmus_641 ,
Nomascus leucogenys	ENSNLEG00000013830	3 retrocopies	retro_nleu_1264, retro_nleu_1530, retro_nleu_586,
Pongo abelii	ENSPPYG00000008741	1 retrocopy	retro_pabe_2312,
Pan troglodytes	ENSPTRG00000009767	1 retrocopy	retro_ptro_1793,
Rattus norvegicus	ENSRNOG00000048712	1 retrocopy	retro_rnor_472,