RetrogeneDB ID: retro_mmus_1198

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:50552867..50553828(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atp6ap1
• Ensembl ID: ENSMUSG00000019087
• Aliases: Atp6ap1, 16A, AC45, AI316502, AW108110, Atp6ip1, Atp6s1, C7-1, CF2, VATPS1, XAP-3, mFLJ00383
• Description: ATPase, H+ transporting, lysosomal accessory protein 1 [Source:MGI Symbol;Acc:MGI:109629]

Sequence

>retro_mmus_1198
GACCTGTAGGCTCCTGTGGCCAACACCCATGAGGGTCATATCACCAGCAATATGCATCTTTCTGCCTACTTAGACCCTGC
CCTGGAACTGGGCCCCTGCAATGTACTGCTGCTCCTGCAGGACAAGATAAGCATTGAGGATTTCAGAGCATATGGTGGTA
TGTTTGAAATAAGCAGGAGAGTGCCTTTTCTAACCTGGAGAGTGCCCTGGACTTGGTCCCCTCTTCACTGGTACTTCCTG
CTGTGGACTACTGTGCAATCAGCACTCTGACCACCTACCTACAGGGAAGCTTGGGACTAGTCCCCTGAATGTGGATATAG
CTACCCTAAAGGAGCTGAAGTTCAATATCAGCCTTCCTACTTGCTGCCCATCTGTCTGCCCTAACAGCCAGCTCCAGTTT
GAGGGTGCCCATAGAGGTTATCACAGGTAAAGATGAGTCCATCAGACGTGTGTTGAGCATACTCAAGTCTGAAGATGTCC
CTTAAACCATAGTTCTTACTTCAGTCTGCCCTTCTAGAGTGGCCCATGGTATAGCCATGGTGGCTGGGAGTCTAGGTTAC
CAGCTGCTTCAGACTCAGGTGGCATCACTTGTGATCCATTCTCCTGTGAGTTACAATGACATTGCCCCAAGGATCCTTAT
TTGGGCACAAAACTTCTCTATGGCATACAAAGAGTGGAAAGTCTTGACCTCCCTCGCCTTTGGTGTTGAAAATCTTAACA
TGACCAGCTCCATCTGGAATGACTCCTTTACCATGCTTTCACTGACCTATGAGCCACTCTTTGGCACAACAGTGGCATTC
CAGTTCATTCTGGCTAGTCGCTTCTACCCAGTATCTGGCCAGTATTGGTTTACCATGGAATGACTTGGAATCCATAGCAA
TGGCTCTGTTGCTCACTTCAATGTTCCCAAGTCACAGGACCTAGGATCTATTCTTTCCACTTTGATTATGTTAGCAGTCT
G

Alignment

ORF - retro_mmus_1198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.52 %
• Parental protein coverage: 69.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NLWAPVADTHEGHITSDMQLSTYLDPALELGPRNVLLFLQDKLSIEDFTAYGGVFG-NKQDSAFSNLENA
          .L.APVA.THEGHITS.M.LS.YLDPALELGP.NVLL.LQDK.SIEDF.AYGG.F..NKQ.SAFSNLE.A
Retrocopy DL*APVANTHEGHITSNMHLSAYLDPALELGPCNVLLLLQDKISIEDFRAYGGMFE<NKQESAFSNLESA

Parental  LDLAPSSLVLPAVDWYAISTLTTYLQE-KLGASPLHVDLATLKELKLNASLPA-LLLIRLP-YTASSGLM
          LDL.PSSLVLPAVD..AISTLTTYLQ..KLG.SPL.VD.ATLKELK.N.SLP..LL.I.LP..TASS.L.
Retrocopy LDLVPSSLVLPAVDYCAISTLTTYLQG<KLGTSPLNVDIATLKELKFNISLPT<LLPICLP<LTASSSLR

Parental  APREVLTGNDEVIGQVLSTLKSEDVPYTAALTAVRPSRVARDITMVAGGLGRQLLQTQVASPAIHPPVSY
          .P.EV.TG.DE.I..VLS.LKSEDVP.T..LT.V.PSRVA..I.MVAG.LG.QLLQTQVAS..IH.PVSY
Retrocopy VPIEVITGKDESIRRVLSILKSEDVP*TIVLTSVCPSRVAHGIAMVAGSLGYQLLQTQVASLVIHSPVSY

Parental  NDTAPRILFWAQNFSVAYKDEWKDLTSLTFGVENLNLTGSFWNDSFAMLSLTYEPLFGATVTFKFILASR
          ND.APRIL.WAQNFS.AYK.EWK.LTSL.FGVENLN.T.S.WNDSF.MLSLTYEPLFG.TV.F.FILASR
Retrocopy NDIAPRILIWAQNFSMAYK-EWKVLTSLAFGVENLNMTSSIWNDSFTMLSLTYEPLFGTTVAFQFILASR

Parental  FYPVSARYWFAMERLEIHSNGSVAHFNV-SQVTGPSIYSFHCEYVSSV
          FYPVS..YWF.ME.L.IHSNGSVAHFNV.SQVTGP.IYSFH..YVSS.
Retrocopy FYPVSGQYWFTME*LGIHSNGSVAHFNV<SQVTGPRIYSFHFDYVSSL

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	306.43 RPM
SRP007412_cerebellum	0.00 RPM	262.05 RPM
SRP007412_heart	0.00 RPM	116.99 RPM
SRP007412_kidney	0.00 RPM	175.15 RPM
SRP007412_liver	0.00 RPM	64.37 RPM
SRP007412_testis	0.00 RPM	14.13 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1198 was not detected

EST

No EST(s) were mapped for retro_mmus_1198 retrocopy.

TSS

No TSS is located nearby retro_mmus_1198 retrocopy 5' end.

Lab

retro_mmus_1198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1198 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000008869	1 retrocopy	retro_mdom_1068,
Mus musculus	ENSMUSG00000019087	1 retrocopy	retro_mmus_1198 ,
Oryctolagus cuniculus	ENSOCUG00000017631	1 retrocopy	retro_ocun_863,
Sarcophilus harrisii	ENSSHAG00000005317	1 retrocopy	retro_shar_519,