RetrogeneDB ID: retro_mmus_544

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:30373878..30374514(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mkrn2
• Ensembl ID: ENSMUSG00000000439
• Aliases: Mkrn2, 2610002L04Rik, C81377
• Description: makorin, ring finger protein, 2 [Source:MGI Symbol;Acc:MGI:1914277]

Sequence

>retro_mmus_544
GACCCAGAACAAAGGAAAGCTCATGAGAAGATGTGTATGTTGACATTTGAACATGAGATGGACAAGGCGTTTGCCTTCCA
GGCGAGCCAGGACAAAGTGTGCAGCATCTGTATGGAGGTGATCCTTGAGAAAGCATCTGCTTTTGAGAGGAGTTTTGGCG
TTCTCTCCAACTGCAGCCGCACCTACTGCCTGTCCTGCATCCATCAATGGCAATGTGCCAAACAGTTTGAAAACCTGATC
ATAAAGTCTTGTCCAGAGTGCCGTGTGATATCAGAGTTTGTAATTCCAAGTGTGTATTGGGTAGAAAATCGGAATAAAAG
GAATGAATTAATTGAAGCTTTCAAACGGGGAATGAGGGAAAAGGCATGTAAATACTTTGAACAAGACAAGGGGACCTGCC
CCTTTGGAAGCAAGTGCCTTTACCACCATGCTTACCCTCATGGGCGGCTGGCAGAGCCAGAGAAACCTCGGAAGCAGCTA
AACTCTGAAGGAACTGTGAGGTTCTTTAACTCAGTGTGGCTTTGGGATTTTATCGAGAACCAAGAAACCCGGCAAGTCCC
CAGCACTGATAATGTGGATGTGATAGTGCTAGGAGGCCTTTTCATGCACCTTTCTGGAGTAGAGTCATCAGAACCC

Alignment

ORF - retro_mmus_544 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.21 %
• Parental protein coverage: 50.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DPEQRKAHEKMCMSTFEHEMEKAFAFQASQDKVCSICMEVILEKASASERRFGILSNCSHTYCLSCIRQW
          DPEQRKAHEKMCM.TFEHEM.KAFAFQASQDKVCSICMEVILEKASA.ER.FG.LSNCS.TYCLSCI.QW
Retrocopy DPEQRKAHEKMCMLTFEHEMDKAFAFQASQDKVCSICMEVILEKASAFERSFGVLSNCSRTYCLSCIHQW

Parental  RCAKQFENPIIKSCPECRVISEFVIPSVYWVEDQNKKNELIEAFKQGMGKKACKYFEQGKGTCPFGSKCL
          .CAKQFEN.IIKSCPECRVISEFVIPSVYWVE..NK.NELIEAFK.GM..KACKYFEQ.KGTCPFGSKCL
Retrocopy QCAKQFENLIIKSCPECRVISEFVIPSVYWVENRNKRNELIEAFKRGMREKACKYFEQDKGTCPFGSKCL

Parental  YRHAYPDGRLAEPEKPRKQLSSEGTVRFFNSVRLWDFIENRETRQVPSTDDVDVTELGDLFMHLSGVESS
          Y.HAYP.GRLAEPEKPRKQL.SEGTVRFFNSV.LWDFIEN.ETRQVPSTD.VDV..LG.LFMHLSGVESS
Retrocopy YHHAYPHGRLAEPEKPRKQLNSEGTVRFFNSVWLWDFIENQETRQVPSTDNVDVIVLGGLFMHLSGVESS

Parental  EP
          EP
Retrocopy EP

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	0.02 RPM	20.19 RPM
SRP007412_cerebellum	0.00 RPM	19.76 RPM
SRP007412_heart	0.00 RPM	26.99 RPM
SRP007412_kidney	0.00 RPM	18.23 RPM
SRP007412_liver	0.00 RPM	9.99 RPM
SRP007412_testis	0.00 RPM	62.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_544 was not detected

EST

No EST(s) were mapped for retro_mmus_544 retrocopy.

TSS

No TSS is located nearby retro_mmus_544 retrocopy 5' end.

Lab

retro_mmus_544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_544 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016733	1 retrocopy	retro_cjac_2362,
Mus musculus	ENSMUSG00000000439	2 retrocopies	retro_mmus_3578, retro_mmus_544 ,
Mus musculus	ENSMUSG00000029922	1 retrocopy	retro_mmus_2663,
Otolemur garnettii	ENSOGAG00000003255	1 retrocopy	retro_ogar_3196,
Pteropus vampyrus	ENSPVAG00000005822	1 retrocopy	retro_pvam_1177,