RetrogeneDB ID: retro_mmus_332

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:69377297..69378204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pced1a
• Ensembl ID: ENSMUSG00000037773
• Aliases: Pced1a, A930025D01Rik, AI480484, Fam113a
• Description: PC-esterase domain containing 1A [Source:MGI Symbol;Acc:MGI:2442177]

Sequence

>retro_mmus_332
ATGCCCCATCTCCGAGCTCACGAAGTCCAGCAGCTGTTGCACAACAAGTTCGTCGTCGTCCTGGGGGACTCGATCCAGAG
AGCCGTCTACAAGGACTTGGTGCTCCTGCTCCAGAAGGACTGCCTGCTGTCTTCCAGCCAGCTGAAGAGCAAGGGCGAGC
TGAGCTTCGAACGCGACGTACTGCTGGAGGGCGGCAGATGGGGACGCATGCACAATGGCGCCCACTACCGCGAGGTGCGC
CAGTTCTGCTCCGGGCGCCACTTGATACGCTTCTATTTCCTCACGCGGGCCTACTCGCCCTATGTTGAGGACATCCTGCA
GCAGCTGCGATGGGGCGAGTATGCCCCCGACTTGGTGATCATGAACTCATGCCTCTGGGACCTGTCCAGGTACAGAAGCA
ATTTCCTCAGAAACTACCGAGAGGACTTGGAGAGGCTTTTCCAACGCCTGGATCAGGTGCTGCCCACCCACTGCCTCATG
GTATGGAGTACCACCATGCCTGTGGCCGAGGTCGTGTCCGGGGGCTTCATCCTGCGGGATGCCCCAGGGTGCCCCTCACG
CCTGCGTGAAGATGTGATGGAGGCCAACTTTTACAGCTCCAGGGAGGCGGCGAGGCGTGGCTTCGATGTGCTGGATCTCC
ACTTCCACTTCCGCCATGCAGGGCAGCATCGGCTGAGCGATGGCGTGCACTGGGATGAGCGAGCGCACCGCTACCTCTCG
CAGCTGCTGCTCGCCCATGTGGCAGACGCCTGGGGTGTGATCCTCCCAGCCCACAACCCCGTGGGAAGGTGGATCAGGGA
TGGTCCTGTAGGAAGACAGCCAGACCGGGCAGACCGAAGGCATCCTCGAGACCACCACCGCCATGAGCAGCGTGAACCTC
CTGGGGCCAGGCATTCTCCCGCTCCCA

Alignment

ORF - retro_mmus_332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.11 %
• Parental protein coverage: 67.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVHFHASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDTLLTASQLKAKGELSFEQDQLVAGGQLGEL
          M.H..A.EVQQLLHNKFVV.LGDSIQRAVYKDLVLLLQKD.LL..SQLK.KGELSFE.D.L..GG..G..
Retrocopy MPHLRAHEVQQLLHNKFVVVLGDSIQRAVYKDLVLLLQKDCLLSSSQLKSKGELSFERDVLLEGGRWGRM

Parental  HNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDILEELSYGP-APDLVIINSCLWDLSRYGRCSMES
          HNG..YREVRQFCSG...HL.RFYFLTR.YS.Y.EDIL..L..G..APDLVI.NSCLWDLSRY.......
Retrocopy HNGAHYREVRQFCSG--RHLIRFYFLTRAYSPYVEDILQQLRWGEYAPDLVIMNSCLWDLSRYRSNFLRN

Parental  YRENLERVFVRMDQVLPDSCLLVWNLAMPLGERVTGGFLLPELQPLAVSLRQDVVEGNFYSATLAGKHCF
          YRE.LER.F.R.DQVLP..CL.VW...MP..E.V.GGF.L.........LR.DV.E.NFYS...A....F
Retrocopy YREDLERLFQRLDQVLPTHCLMVWSTTMPVAEVVSGGFILRDAPGCPSRLREDVMEANFYSSREAARRGF

Parental  DVLDLHFHFRHAVRHRHRDGVHWDQHAHRHLSHLLLAHVADAWGVELPKHDRLPDPWIEDWSEMDHSFQG
          DVLDLHFHFRHA..HR..DGVHWD..AHR.LS.LLLAHVADAWGV.LP.H......WI.D..........
Retrocopy DVLDLHFHFRHAGQHRLSDGVHWDERAHRYLSQLLLAHVADAWGVILPAHNPV-GRWIRDGPVGRQPDRA

Parental  SHKQPPDFRE-KLALPLLPPFHLPPP
          ....P.D.........LL.P..LP.P
Retrocopy DRRHPRDHHR>MSSVNLLGPGILPLP

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	15.56 RPM
SRP007412_cerebellum	0.00 RPM	15.94 RPM
SRP007412_heart	0.00 RPM	9.09 RPM
SRP007412_kidney	0.02 RPM	12.07 RPM
SRP007412_liver	0.03 RPM	13.30 RPM
SRP007412_testis	0.37 RPM	29.09 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_332 was not detected

EST

No EST(s) were mapped for retro_mmus_332 retrocopy.

TSS

No TSS is located nearby retro_mmus_332 retrocopy 5' end.

Lab

retro_mmus_332 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_332 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2207
Pongo abelii	retro_pabe_2080
Macaca mulatta	retro_mmul_341

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343, retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163, retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333, retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332 ,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190, retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,