RetrogeneDB ID: retro_mmus_1578

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:53746343..53746937(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ckb
• Ensembl ID: ENSMUSG00000001270
• Aliases: Ckb, B-CK, Bck, Ck-3, Ck3, Ckbb
• Description: creatine kinase, brain [Source:MGI Symbol;Acc:MGI:88407]

Sequence

>retro_mmus_1578
TACATCATGACAGTGGGTGCAGTGGCAGGCGACGAGGAGAGGCACGACTTATTCAAGGACTTCTTCAACCCCATTATTGA
GGAGCAGCATGGAGGCTACCAGCCCAGTGATGCACACAAGACCGACCTCAACCCAGACAACCTGCACGGTGGTGATGGCC
TGGACCCCAACTATGTGCTGAGCTCCCAGGTGCACACAGGCCGCAGCATCCACTGCCTTTGTCTCCCTCTGCACTGCAGC
CGCGGGGAACGCTGCGCCATCCCGAAGCTGGCAGTAGAAGCTCTGTCCAGACTAGATTGCTACCTGTCTGGCAGGTTCTA
AGCGCTCAAGAGCATGACATAGGCGGAGTAGCAGCAGCTCACTGAAGACCACTTCCTCTTCGACAAGCCTGTGTCGCCTC
TGCTGCTGGCCTCCAGCATGGCCTGCGACTGGCTGGATGCTCGCGGCATATGACACAATGACAATAAGACTTTCCTGGTG
TGGATCAATGAGGAGGAACACCTGCGGGTCATCTCCATGCAGAAGGGGTGGGGGGGCAACATGAAGGAAGTGTTCACCCG
ATTCTGCACCGGCCTCACTCAGAAAAACTCTCTT

Alignment

ORF - retro_mmus_1578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 51.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YIMTVGAVAGDEESYDVFKDLFDPIIEERHGGYQPSDEHKTDLNPDNLQGGDDLDPNYVLSSRVRTGRSI
          YIMTVGAVAGDEE..D.FKD.F.PIIEE.HGGYQPSD.HKTDLNPDNL.GGD.LDPNYVLSS.V.TGRSI
Retrocopy YIMTVGAVAGDEERHDLFKDFFNPIIEEQHGGYQPSDAHKTDLNPDNLHGGDGLDPNYVLSSQVHTGRSI

Parental  RGFCLPPHCSRGERRAIEKLAVEALSSLDGDLSGRYYALKSMTEAEQQQLIDDHFLFDKPVSPLLLASGM
          ...CLP.HCSRGER.AI.KLAVEALS.LD..LSGR..ALKSMT.AE.QQL..DHFLFDKPVSPLLLAS.M
Retrocopy HCLCLPLHCSRGERCAIPKLAVEALSRLDCYLSGRF*ALKSMT*AE*QQLTEDHFLFDKPVSPLLLASSM

Parental  ARDWPDARGIWHNDNKTFLVWINEEDHLRVISMQK--GGNMKEVFTRFCTGLTQIETL
          A.DW.DARGI.HNDNKTFLVWINEE.HLRVISMQK..GGNMKEVFTRFCTGLTQ...L
Retrocopy ACDWLDARGI*HNDNKTFLVWINEEEHLRVISMQKGWGGNMKEVFTRFCTGLTQKNSL

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	643.25 RPM
SRP007412_cerebellum	0.17 RPM	739.20 RPM
SRP007412_heart	0.00 RPM	39.54 RPM
SRP007412_kidney	0.00 RPM	47.07 RPM
SRP007412_liver	0.00 RPM	3.71 RPM
SRP007412_testis	0.00 RPM	3.61 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1578 was not detected

EST

No EST(s) were mapped for retro_mmus_1578 retrocopy.

TSS

No TSS is located nearby retro_mmus_1578 retrocopy 5' end.

Lab

retro_mmus_1578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1578 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018277	5 retrocopies	retro_cfam_1828, retro_cfam_2061, retro_cfam_2159, retro_cfam_274, retro_cfam_664,
Ciona intestinalis	ENSCING00000007141	1 retrocopy	retro_cint_27,
Echinops telfairi	ENSETEG00000008667	1 retrocopy	retro_etel_1667,
Macropus eugenii	ENSMEUG00000002979	3 retrocopies	retro_meug_1069, retro_meug_1569, retro_meug_2156,
Mus musculus	ENSMUSG00000001270	4 retrocopies	retro_mmus_1460, retro_mmus_1578 , retro_mmus_1647, retro_mmus_2390,
Sarcophilus harrisii	ENSSHAG00000016459	2 retrocopies	retro_shar_432, retro_shar_645,