RetrogeneDB ID: retro_mmus_2149

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:36421617..36422124(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cd164
• Ensembl ID: ENSMUSG00000019818
• Aliases: Cd164, A115, A24, AA589639, AW540279, MGC-24, MSSP
• Description: CD164 antigen [Source:MGI Symbol;Acc:MGI:1859568]

Sequence

>retro_mmus_2149
CTCACTGAGCTCTGCATGTCTACCTCACAGCACAACAGCAACGTAGCTAATGTGACTGAGTCGCTGACCATGACCACCAA
GCTGCCAGAAACCTGTGAGAGCTTCAACAGCTGTGTTTCCTGTGTTAATGCCACCATTACTAATAATATTACCTGAGCTT
GGATAGATTGCCAAGAAGCAAATAAGACCTATTGTTCATGTGAATTAGTAAGTGATTGTACCCAAGTGAACAGCACTGAC
TTCTGCTCTGTAGTACCTCCGACCGCTCCAGTGCCAACCAAGTCTACAGCTAAACCCACAACTCAGCCTTCCTCTCCTAC
ACTTACTCCCTCAGTTGTCATATCACCAGGTACAGCAAATACCACTCTGACTCCAACCTCACAACCTGCGAGAAAGTCTA
CCTATTCCAGCCTCATTGGAGGGATCGTCCTTGTCTTCAGTGTGCAGGCTGTAATTTTCTTTCTCTATAAGTTCTGCAAA
TCTAAAGAATGAAATTACCATACTCTG

Alignment

ORF - retro_mmus_2149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.01 %
• Parental protein coverage: 86.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITTLAPNVTEVPTTTTKVVPTTQMPTVLPETCASFNSCVSCVNATFTNNITCFWLHCQEANKTYCANEPL
          .T.L.............V.....M.T.LPETC.SFNSCVSCVNAT.TNNIT..W..CQEANKTYC..E..
Retrocopy LTELCMSTSQHNSNVANVTESLTMTTKLPETCESFNSCVSCVNATITNNIT*AWIDCQEANKTYCSCELV

Parental  SNCSQVNRTDLCSVIPPTTPVPTNSTAKPTTRPSSPTPTPSVVTSAGTTNTTLTPTSQPERKSTFDAASF
          S.C.QVN.TD.CSV.PPT.PVPT.STAKPTT.PSSPT.TPSVV.S.GT.NTTLTPTSQP.RKST....S.
Retrocopy SDCTQVNSTDFCSVVPPTAPVPTKSTAKPTTQPSSPTLTPSVVISPGTANTTLTPTSQPARKSTY--SSL

Parental  IGGIVLVLGVQAVIFFLYKFCKSKERNYHTL
          IGGIVLV..VQAVIFFLYKFCKSKE.NYHTL
Retrocopy IGGIVLVFSVQAVIFFLYKFCKSKE*NYHTL

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	57.89 RPM
SRP007412_cerebellum	0.00 RPM	52.02 RPM
SRP007412_heart	0.00 RPM	94.14 RPM
SRP007412_kidney	0.00 RPM	251.36 RPM
SRP007412_liver	0.00 RPM	238.29 RPM
SRP007412_testis	0.05 RPM	115.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2149 was not detected

EST

No EST(s) were mapped for retro_mmus_2149 retrocopy.

TSS

No TSS is located nearby retro_mmus_2149 retrocopy 5' end.

Lab

retro_mmus_2149 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2149 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000019818	1 retrocopy	retro_mmus_2149 ,
Ochotona princeps	ENSOPRG00000014063	3 retrocopies	retro_opri_1015, retro_opri_1045, retro_opri_60,