RetrogeneDB ID: retro_mmus_1217

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:74297556..74298765(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nasp
• Ensembl ID: ENSMUSG00000028693
• Aliases: Nasp, 5033430J04Rik, AI131596, AI317140, D4Ertd767e, Epcs32, Nasp-T
• Description: nuclear autoantigenic sperm protein (histone-binding) [Source:MGI Symbol;Acc:MGI:1355328]

Sequence

>retro_mmus_1217
GATGTGGATAGTGAAGCTAAGAAACTACTGGGACTAGGACAGAAACATCTGGTGATGGGTGACATTCTAGCAACTGTTAA
TGCATTCCAGGAAGCAGTTAGTCTTTTAGGTAAAAAGTATGGAAAAACAGCTAATGAGTGTGGAGAAGCATTCTTTTATT
TATGGGAAATCACTTCAGGAGTTGGCCAGAATGAAGACTGGAGTGTTGGGAAATGTCTTAGAAGGAGTGCATATAGAAGA
GGAAGAAGGAGAAAAAAACAGAAGATGAATCTTTGGTCGAAAATAATAATAATGTAGATGAAACTGAAGGCTCAGAGGAA
GAAGACAAAGAAAATGACAAGGCTGAAGAAACAACAAATAAACCAGTTCTTGAAAAAAAATTCTCCTCAAGAAAATGAAG
AGGAAGAGATTGGGAATTTAGAACTTGCCTGGGATATGCTGGATTTAGCCAAGATCATTTTTAAGAGGCAAGAAACAAAA
GAAGCCCAGTTTTATGCTGCACAAACCCATCTTAAACTTAGAGAAGTTAGTGTTGAATCTGAGAATTATATCCAAAGAGG
AGGATAGTTTCAGGCTTGCTGAAGCCTAAAAGAACAATATTTGGAAGCTCACGATTGTCTCCTTGCAGAGACTCACTACC
AGTTGGGTTTGGCCAATGGTTACAGCTCTCAGTGTAATGAGGCAGTAGCACAGTTTGGCAAATCTATTGAAGTCGTTGAG
AAGAGGATTGCTGTACTACACGAGCAGATGAGGAGGCTAAAGGAACATTTACTGAATATGAGAAAGAAATTGAGGAGCTG
AAAGAACTGCTACCTGAAATTCAAAGGAAGATAGAAGATGCAAAGGAATCTCAGTGGAGTAGGGATGGAGCTGAACTGGC
CTACATCCTCAGGGAATGAAAACTACTCTGGTGGGGAGCTCTACTTCGGGTTTCACTCCTAGTGGAGCCTGTGCTTCAGT
ATCCATGATAGCCAGTAGAAAACCAACAGATGGCACTTCCTCATCAAACTGTGTGATTGATATTTCCCATCTTGTCAGAA
AGAAGAGGAAACCAGGGGAAGAGAGTGCCCGACAAGATGATACAAAGAAAGCTAAACAAGAGCCAGAGGTGACTGGAGGC
AGTGGGGATGCTGTCTCCAGGGGAAATGAAGTTTCAGAAAACATGGAGGCTGAAACTGAGAACAGGCTGAGAGCCAGACA
ACAGAAGGG

Alignment

ORF - retro_mmus_1217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.46 %
• Parental protein coverage: 88.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  DVDSEAKKLLGLGQKHLVMGDIPAAVNAFQEAASLLGKKYGETANECGEAFFF-YGKSLLELARMENGVL
          DVDSEAKKLLGLGQKHLVMGDI.A.VNAFQEA.SLLGKKYG.TANECGEAFF..YGKSL.ELARM..GVL
Retrocopy DVDSEAKKLLGLGQKHLVMGDILATVNAFQEAVSLLGKKYGKTANECGEAFFY>YGKSLQELARMKTGVL

Parental  GNALEGVHVEEEEGEK-TEDESLVENNDNVDETEGSEEEDRENDKAEETPNESVLEKK-SLQENEEEEIG
          GN.LEGVH.EEEEGEK.TEDESLVENN.NVDETEGSEEED.ENDKAEET.N..VL....S.QENEEEEIG
Retrocopy GNVLEGVHIEEEEGEK>TEDESLVENNNNVDETEGSEEEDKENDKAEETTNKPVLXXX>SPQENEEEEIG

Parental  NLELAWDMLDLAKIIFKRQETKEAQLYAAQAHLKLGEVSVESENYIQAVEEFQACLSLQEQYLEAHDRLL
          NLELAWDMLDLAKIIFKRQETKEAQ.YAAQ.HLKL.EVSVESENYIQ....FQAC.SL.EQYLEAHD.LL
Retrocopy NLELAWDMLDLAKIIFKRQETKEAQFYAAQTHLKLREVSVESENYIQRGG*FQAC*SLKEQYLEAHDCLL

Parental  AETHYQLGLAYGYNSQYDEAVAQFGKSIDVIEKRMAVLHEQMK-EAEGSFTEYEKEIEELKELLPEIREK
          AETHYQLGLA.GY.SQ..EAVAQFGKSI.V.EKR.AVLHEQM..EA.G.FTEYEKEIEELKELLPEI..K
Retrocopy AETHYQLGLANGYSSQCNEAVAQFGKSIEVVEKRIAVLHEQMR<EAKGTFTEYEKEIEELKELLPEIQRK

Parental  IEDAKESQRSGNVAELA-LKATLVESSTSGFTPSG---AGASVSM--IASRKPTDGASSSNCVTDISHLV
          IEDAKESQ.S...AELA.L..........G...SG....GA..S...IASRKPTDG.SSSNCV.DISHLV
Retrocopy IEDAKESQWSRDGAELA<LHPQGMKTTLVGSSTSGFTPSGACASVSMIASRKPTDGTSSSNCVIDISHLV

Parental  RKKRKPEEESPRKDDAKKAKQEPEVNGGSGDAVSSGKEVSENMEAEAEN-QAESQTAEG
          RKKRKP.EES.R.DD.KKAKQEPEV.GGSGDAVS.G.EVSENMEAE.EN.QAESQT.EG
Retrocopy RKKRKPGEESARQDDTKKAKQEPEVTGGSGDAVSRGNEVSENMEAETEN<QAESQTTEG

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	19.39 RPM
SRP007412_cerebellum	0.09 RPM	19.41 RPM
SRP007412_heart	0.00 RPM	17.68 RPM
SRP007412_kidney	0.06 RPM	21.46 RPM
SRP007412_liver	0.00 RPM	14.12 RPM
SRP007412_testis	0.14 RPM	1227.41 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1217 was not detected

EST

No EST(s) were mapped for retro_mmus_1217 retrocopy.

TSS

No TSS is located nearby retro_mmus_1217 retrocopy 5' end.

Lab

retro_mmus_1217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1217 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010436	1 retrocopy	retro_chof_2560,
Homo sapiens	ENSG00000132780	1 retrocopy	retro_hsap_4064,
Macropus eugenii	ENSMEUG00000001037	1 retrocopy	retro_meug_1359,
Mus musculus	ENSMUSG00000028693	1 retrocopy	retro_mmus_1217 ,
Nomascus leucogenys	ENSNLEG00000014434	1 retrocopy	retro_nleu_564,
Pongo abelii	ENSPPYG00000001409	1 retrocopy	retro_pabe_3338,
Pan troglodytes	ENSPTRG00000000677	1 retrocopy	retro_ptro_2754,