RetrogeneDB ID: retro_mmus_1740

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:79934331..79935561(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zdhhc6
• Ensembl ID: ENSMUSG00000024982
• Aliases: Zdhhc6, 2400007G07Rik, 5930409M18Rik, AI462345, C77369
• Description: zinc finger, DHHC domain containing 6 [Source:MGI Symbol;Acc:MGI:1914230]

Sequence

>retro_mmus_1740
ATGGGCTTATTCTGCTCAGGAATCAAGTTTGAAAATCTTCAAGACTTAAGGAGACTGTGTCACTGGGGTCCCATCATATC
CCTGGGTGTTATAGCAATATGTTCCACAATGGCCATGATCGACTCTGTCTTGTGGTATTGGCCCTTACATACAACTGGAG
GAAATGTGAACTTCATCATGTTGATAAATTGGACCGTCATGATTCTTTATAATTACTTCAATGCCATGTTTGCTGGTCCT
GGCTTCGTCCCTCGGGGATGGAAACCGGAAAAGTCTCAGGATAGCATGTATCTCTAGTATTGTAAAGTCTGCCAAGCACA
CAAGGCGCCACGTTCACATCATTGCAGAAAGTGTAACAGATGTGTAATGAAGATGGACCACCGCTGCCTCTGGATCAACA
ACTGCTGTGGTCACCAGAACCACGCCTCGTTCACACTCTCCCTTCTGTTGGCCCCTCTGGGCTGCACCCATGCTGCTTTC
ATCTTCGTGATGACAATGTACACACAGCTTTATAATCGGCTCTCCTTTGGGTGGAACACAGTCAAGATTGACATGAGTGC
AGCCAGGGGAGATCCACCTCCAATTGTTCCCTTCAGATTGGCTGCATTTGCCACCATCTTGTTTGCCCTGGGATTAGCTT
TGGGAACAACCATAGCTGTTGGGATGTTGTTTTTCATACAGATAAAAATTATTCTCAGAAACAAAACTTCTATTGAATCA
TGGATTGAAGAAAAGGCTAACGATCGCATTCAGTATTACCAACTGAGTGAAGTCTTCATTTTTCCTTATGATATGGGAAG
TAAGTGGAAGAACTTTAAACAGGTGTTTACATGGTCTGGAGTCCCTGAAGGAGATGGACTTGAGTGGCCAATATGAGAGG
GCTGTGACCAGTACAGCCTCACAATAGAACCGTTGAAGCAAAAAGCAGACAAGAGAGTCAGAAGTGTTCGCTATAAAGTC
ATAGAAGACTACAATGGTGCCTGCTGCCCTTTGAATAGAGGAGTGAGAACCTTCTTTACAAGCCCCTGCACTGAGGATCC
TCAGATACGGCTGCAGAAAGGAGAGTTCATCTTAGCAACAAGAGGGTTATGATACTGGTTGTATGGAGACAAAATTCTTG
ATGATTCCTTCATAGAAGGTACTTCAAGAGTAAGAGGGTGGTTTCCTAGAAACTGTGTGGAAAAGTGTCCCTGTGATAGT
GACTCAGATCCAGCCCCAGAGGGGGAGAAG

Alignment

ORF - retro_mmus_1740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.88 %
• Parental protein coverage: 99.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGIFCSVIKFENLQDLRRLCHWGPIIALGVIAICSTMAMIDSVLWYWPLHTTGGSVNFIMLINWTVMILY
          MG.FCS.IKFENLQDLRRLCHWGPII.LGVIAICSTMAMIDSVLWYWPLHTTGG.VNFIMLINWTVMILY
Retrocopy MGLFCSGIKFENLQDLRRLCHWGPIISLGVIAICSTMAMIDSVLWYWPLHTTGGNVNFIMLINWTVMILY

Parental  NYFNAMFAGPGFVPRGWKPEKSQDSMYLQYCKVCQAYKAPRSHHCRKCNRCVMKMDHHCPWINNCCGHQN
          NYFNAMFAGPGFVPRGWKPEKSQDSMYL.YCKVCQA.KAPRSHHCRKCNRCVMKMDH.C.WINNCCGHQN
Retrocopy NYFNAMFAGPGFVPRGWKPEKSQDSMYL*YCKVCQAHKAPRSHHCRKCNRCVMKMDHRCLWINNCCGHQN

Parental  HASFTLFLLLAPLGCTHAAFIFVMTMYTQLYNRLSFGWNTVKIDMSAARRDPPPIVPFGLAAFAATLFAL
          HASFTL.LLLAPLGCTHAAFIFVMTMYTQLYNRLSFGWNTVKIDMSAAR.DPPPIVPF.LAAFA..LFAL
Retrocopy HASFTLSLLLAPLGCTHAAFIFVMTMYTQLYNRLSFGWNTVKIDMSAARGDPPPIVPFRLAAFATILFAL

Parental  GLALGTTIAVGMLFFIQIKIILRNKTSIESWIEEKAKDRIQYYQLDEVFIFPYDMGSKWKNFKQVFTWSG
          GLALGTTIAVGMLFFIQIKIILRNKTSIESWIEEKA.DRIQYYQL.EVFIFPYDMGSKWKNFKQVFTWSG
Retrocopy GLALGTTIAVGMLFFIQIKIILRNKTSIESWIEEKANDRIQYYQLSEVFIFPYDMGSKWKNFKQVFTWSG

Parental  VPEGDGLEWPIREGCDQYSLTIEQLKQKADKRVRSVRYKVIEDYNGACCPLNRGVRTFFTSPCTEEPRIR
          VPEGDGLEWPI.EGCDQYSLTIE.LKQKADKRVRSVRYKVIEDYNGACCPLNRGVRTFFTSPCTE.P.IR
Retrocopy VPEGDGLEWPI*EGCDQYSLTIEPLKQKADKRVRSVRYKVIEDYNGACCPLNRGVRTFFTSPCTEDPQIR

Parental  LQKGEFILATRGLRYWLYGDKILDDSFIEGTSRVRGWFPRNCVEKCPCDGDSDPAPEGEK
          LQKGEFILATRGL.YWLYGDKILDDSFIEGTSRVRGWFPRNCVEKCPCD.DSDPAPEGEK
Retrocopy LQKGEFILATRGL*YWLYGDKILDDSFIEGTSRVRGWFPRNCVEKCPCDSDSDPAPEGEK

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	17.27 RPM
SRP007412_cerebellum	0.04 RPM	16.54 RPM
SRP007412_heart	0.06 RPM	18.15 RPM
SRP007412_kidney	0.12 RPM	39.12 RPM
SRP007412_liver	0.00 RPM	55.00 RPM
SRP007412_testis	0.09 RPM	15.60 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1740 was not detected

EST

No EST(s) were mapped for retro_mmus_1740 retrocopy.

TSS

No TSS is located nearby retro_mmus_1740 retrocopy 5' end.

Lab

retro_mmus_1740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1740 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015401	1 retrocopy	retro_amel_1120,
Canis familiaris	ENSCAFG00000010960	1 retrocopy	retro_cfam_2178,
Choloepus hoffmanni	ENSCHOG00000012828	1 retrocopy	retro_chof_1480,
Felis catus	ENSFCAG00000030784	1 retrocopy	retro_fcat_1193,
Loxodonta africana	ENSLAFG00000008129	1 retrocopy	retro_lafr_304,
Mustela putorius furo	ENSMPUG00000002043	1 retrocopy	retro_mputfur_668,
Mus musculus	ENSMUSG00000024982	1 retrocopy	retro_mmus_1740 ,
Otolemur garnettii	ENSOGAG00000030535	1 retrocopy	retro_ogar_1652,
Ictidomys tridecemlineatus	ENSSTOG00000013840	1 retrocopy	retro_itri_308,
Tarsius syrichta	ENSTSYG00000009673	2 retrocopies	retro_tsyr_1653, retro_tsyr_1771,