RetrogeneDB ID: retro_mmus_3191

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:40748002..40749092(-)
• 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_3191
TTGAAAATAGTGGGTGAAGACAACTCAAAAAAATGTATTTTTGTCATCCATGAGCATCTCCTCAGCCCTGGCTATGGTCT
TCATGGGATCAAAAGGAACGATTGAAAGCCAGATGGTTCAGGCACTTTCTTTGGATAAATGCAGTGGCAATGGAGGTAGA
GATGTCCACCAGAGCTTCCAGTTCCTTCTCACCGAAGTGAACAAGACTGGCACACAGTACTTGCTCAGAACAGCCAACAG
GCTCTTTGGAGAAAAGACTTGTGACCTTGTAGCATCTTTAAAAGATTCCTGCCAAAAGTTCTATGAAGCAGAGATGGAAG
AGCTGGACTTAAGGGTGAAACAGAGCAGCCCTGACAGCACATCAACACCTGGATAACCAAAAAAGACAGAAGATAAAATC
AAAGAGCTGCTGTCTCCAGGTACAGTGAATTCTGATACATTGCTATCCCTTGTGAGTGCCATCTACTTCGAAGGAAGCTG
GAAGGAACAGTTCTACAGAGAGGACACCAGGGAGATGCCATTCAAGTCAGCAAGGATGAGAAGAAACCTGTGCAAATGAG
GTTTAAGAAGTCTACCTTTAAGATGACCTATACTGGGGAGATCTTCACTAAGATTCTGTTGCTTCCCTATGTTGGCAATG
AGCTGAACATGATCATCATGCTTCCAGATGAACATGTTGAACTGAGTACGGTGGAAAAGGAAATAACTCATGAGAAATGT
ATAGAGTGAATGAGGCTGGACAAGATGGACGAAGAAGAGGTGGAAGTATTTCTCCCCAAAGTTTAAGCTGGAGGAGAACT
ATGACATGAAGGATGTCTTCTGCAAGCTGGGCATGACTGATGCCTATGAGGGCAGGGCAGACTTTTCTGAAATGTCTTCC
AAGCAAGGTTTGTTTCTGTCTAAGGTTGTGCATAAGGCCTTTGTGGAGGTCAATGAGGAGGGCACAGAGGCTGCAGCTGC
TCCAGCGGTCATCATGATGCTGAGGTGCATGAGGTTCACTCCCCCCTTCTGTGCCTACTGCCCCTTCCTTTTCTTCATTC
ATCATGTTAAGACCGATGTGATTCTGTTCTGTGGCTCGTTCTCCTCTCCC

Alignment

ORF - retro_mmus_3191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.98 %
• Parental protein coverage: 96.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LKILGEDSSK-NVFLSPMSISSALAMVFMGAKGTTASQMAQALALDKCSGNGGGDVHQGFQSLLTEVNKT
          LKI.GED.SK.NVFLS.MSISSALAMVFMG.KGT..SQM.QAL.LDKCSGNGG.DVHQ.FQ.LLTEVNKT
Retrocopy LKIVGEDNSK>NVFLSSMSISSALAMVFMGSKGTIESQMVQALSLDKCSGNGGRDVHQSFQFLLTEVNKT

Parental  GTQYLLRTANRLFGDKTCDLLASFKDSCLKFYEAELEELD-FQGATEESRQHINTWVA-KKTEDKIKEVL
          GTQYLLRTANRLFG.KTCDL.AS.KDSC.KFYEAE.EELD...G.TE...QHINTW...KKTEDKIKE.L
Retrocopy GTQYLLRTANRLFGEKTCDLVASLKDSCQKFYEAEMEELD<LKGETEQP*QHINTWIT>KKTEDKIKELL

Parental  SPGTVNSDTSLVLVNAIYFKGNWEKQFNKEHTREMPFK-VSKNEEKPVQMMFKKSTFKMTYIGEIFTKIL
          SPGTVNSDT.L.LV.AIYF.G.W..QF..E.TREMPFK.VSK.E.KPVQM.FKKSTFKMTY.GEIFTKIL
Retrocopy SPGTVNSDTLLSLVSAIYFEGSWKEQFYREDTREMPFK<VSKDEKKPVQMRFKKSTFKMTYTGEIFTKIL

Parental  LLPYVSSELNMIIMLPDEHVELSTVEKEVTYEKFIEWTRLDKMDEEEVEVFL-PKFKLEENYNMNDALYK
          LLPYV..ELNMIIMLPDEHVELSTVEKE.T.EK.IE..RLDKMDEEEVEVFL.PKFKLEENY.M.D...K
Retrocopy LLPYVGNELNMIIMLPDEHVELSTVEKEITHEKCIE*MRLDKMDEEEVEVFL>PKFKLEENYDMKDVFCK

Parental  LGMTDAFGGRADFSGMSSKQGLFLSKVVHKAFVEVNEEGTEAAAATAGMMTVRCMRFTPRFCADHPFLFF
          LGMTDA..GRADFS.MSSKQGLFLSKVVHKAFVEVNEEGTEAAAA.A..M..RCMRFTP.FCA..PFLFF
Retrocopy LGMTDAYEGRADFSEMSSKQGLFLSKVVHKAFVEVNEEGTEAAAAPAVIMMLRCMRFTPPFCAYCPFLFF

Parental  IHHVKTNGILFCGRFSSP
          IHHVKT..ILFCG.FSSP
Retrocopy IHHVKTDVILFCGSFSSP

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	26.80 RPM
SRP007412_cerebellum	0.00 RPM	29.05 RPM
SRP007412_heart	0.00 RPM	53.36 RPM
SRP007412_kidney	0.04 RPM	42.06 RPM
SRP007412_liver	0.00 RPM	12.43 RPM
SRP007412_testis	0.14 RPM	70.12 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3191 was not detected

EST

No EST(s) were mapped for retro_mmus_3191 retrocopy.

TSS

No TSS is located nearby retro_mmus_3191 retrocopy 5' end.

Lab

retro_mmus_3191 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3191 has 0 orthologous retrocopies within eutheria group .

---

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,