RetrogeneDB ID: retro_mmus_3192

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:40789056..40789756(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Serpinb6a
• Ensembl ID: ENSMUSG00000060147
• Aliases: Serpinb6a, 4930482L21Rik, D330015H01Rik, PI-6, Serpinb6, Spi3, ovalbumin
• Description: serine (or cysteine) peptidase inhibitor, clade B, member 6a [Source:MGI Symbol;Acc:MGI:103123]

Sequence

>retro_mmus_3192
AAAAAGACAGAAGATAAAATCAAAGAGTTGCTGTCTCCAGGTAGAGTGAATTCTGACACATTGCTATTCCTTGTGAATGC
CATCTACTTCATAGGAAACTAGAAGGAACAGTTCTACAGAGAGATTCCATTCAACGTCAGCAAGGATGAGAAGAAAGCTG
TGCAAATGAGGTTTAAGAAGTCTACCTTTAAGATGACCTATACTGGGGAGATCTTCACTAAGATTCTGTTGCTTCCCTAT
GTTGGCAATGAGCTGAACATGATCATCATGCTTCCAGATGAACACGTTGAACTGAGTACAGTGGAAAAGGAAATAACTCA
TGAGAAATGTATAGAGTGAACGAGGCTGGACAAGATGGACGAAGAAGAGGTATAAGTATTTCTCCCCAAAGTTTAAGCTG
GAGGAGAACTATGACATGAAGGATGTCTTCTGCAAGCTGGGCATGACTGATGCCTATGAGGGCAGGGCAGACTTTTCTGA
AATGTCTTCCAAGCAAGGTTTGTTTCTGTCTAAGGTTGTGCATAAGGCCTTTGTGGAGGTCAATGAGGAGGGCACAGAGG
CTGCAGCTGCTCCAGCGGTCATCATGATGCTGAGGTGCATGAGGTTCACTCCCCCCTTCTGTGCCTACTGCCCCTTCCTT
TTCTTCATTCAGGATGTTAAGACCAATGTGATTCTGTTCTGTGGCCCGTTCTCCTCTCCC

Alignment

ORF - retro_mmus_3192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.41 %
• Parental protein coverage: 62.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKTEDKIKEVLSPGTVNSDTSLVLVNAIYFKGNWEKQFNKEHTREMPFKVSKNEEKPVQMMFKKSTFKMT
          KKTEDKIKE.LSPG.VNSDT.L.LVNAIYF.GN...QF..E.....PF.VSK.E.K.VQM.FKKSTFKMT
Retrocopy KKTEDKIKELLSPGRVNSDTLLFLVNAIYFIGN*KEQFYRE----IPFNVSKDEKKAVQMRFKKSTFKMT

Parental  YIGEIFTKILLLPYVSSELNMIIMLPDEHVELSTVEKEVTYEKFIEWTRLDKMDEEEVEVFL-PKFKLEE
          Y.GEIFTKILLLPYV..ELNMIIMLPDEHVELSTVEKE.T.EK.IE.TRLDKMDEEEV.VFL.PKFKLEE
Retrocopy YTGEIFTKILLLPYVGNELNMIIMLPDEHVELSTVEKEITHEKCIE*TRLDKMDEEEV*VFL>PKFKLEE

Parental  NYNMNDALYKLGMTDAFGGRADFSGMSSKQGLFLSKVVHKAFVEVNEEGTEAAAATAGMMTVRCMRFTPR
          NY.M.D...KLGMTDA..GRADFS.MSSKQGLFLSKVVHKAFVEVNEEGTEAAAA.A..M..RCMRFTP.
Retrocopy NYDMKDVFCKLGMTDAYEGRADFSEMSSKQGLFLSKVVHKAFVEVNEEGTEAAAAPAVIMMLRCMRFTPP

Parental  FCADHPFLFFIHHVKTNGILFCGRFSSP
          FCA..PFLFFI..VKTN.ILFCG.FSSP
Retrocopy FCAYCPFLFFIQDVKTNVILFCGPFSSP

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	0.07 RPM	26.80 RPM
SRP007412_cerebellum	0.09 RPM	29.05 RPM
SRP007412_heart	0.00 RPM	53.36 RPM
SRP007412_kidney	0.23 RPM	42.06 RPM
SRP007412_liver	0.05 RPM	12.43 RPM
SRP007412_testis	0.41 RPM	70.12 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3192 was not detected

EST

No EST(s) were mapped for retro_mmus_3192 retrocopy.

TSS

No TSS is located nearby retro_mmus_3192 retrocopy 5' end.

Lab

retro_mmus_3192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3192 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017483	1 retrocopy	retro_btau_827,
Echinops telfairi	ENSETEG00000012630	1 retrocopy	retro_etel_1134,
Microcebus murinus	ENSMICG00000001981	1 retrocopy	retro_mmur_403,
Myotis lucifugus	ENSMLUG00000008803	1 retrocopy	retro_mluc_1610,
Monodelphis domestica	ENSMODG00000005468	2 retrocopies	retro_mdom_510, retro_mdom_602,
Mustela putorius furo	ENSMPUG00000000448	1 retrocopy	retro_mputfur_1037,
Mus musculus	ENSMUSG00000060147	2 retrocopies	retro_mmus_3191, retro_mmus_3192 ,
Pteropus vampyrus	ENSPVAG00000010001	1 retrocopy	retro_pvam_1243,
Tursiops truncatus	ENSTTRG00000003879	2 retrocopies	retro_ttru_1224, retro_ttru_1837,