RetrogeneDB ID: retro_mmus_1001

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:23728970..23730103(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083206
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1001
CAGGGGGAGCTGAGCTTTGCACAGGATCAGCTGGTGGCTGGGGGCCAGCTGGGAGAGCGGCGCAATGGGAAATAGTATTG
CCAGGTCCGCCAGTTCTGCTCTGGTTCTGACCACTACTTTGTGTGCTTCTACTTCCTCACTCGTGTTACTCCGAGTACCT
TGAGGACTTCTTGGAGGAGCTGTGATATGGACCTTCCCCTGACCTAGTGATCATCAACTCCTGACTTTGGGATCTCTCCA
GATATGGCCGCTGCTCAATAGAGAGCTTCAGAGAGAACTTGGAACGAGCGTTTGTACGAATGGACCATGTTTTGCCAGAC
TCTTGTTTGCTGGTGTGGAACTTGGCAATATCTTTTGGGGAAACTTGTCACTGGAGGTTTCTTTCTGCCAGGCTCCAGCC
CTTGGCCGTCTCTCTGCTACAGGATGTGGTTGAGAGGAACTTCTACAAAGCTACACTAGCAGGGAACTACTGTTTCGTTG
TCCTAGATCTCCAATTCCGTTTCCAGCATTGTTGTACACCACCGTCATCGAGATTGTGTCCATTGGGACCAGCATGCACA
CCGCCACCTCTCACACTTACTTCTGACCCACTGGGCTGTGGAGCCACCTAAACATGGCCATCTCCCAGACCTGTGGGTTG
AGGTCTGGCCAGAGATGGATCATTCATTCCAGGGAAGCCATTAAACAGCCCCCAGACTTCAGAGAGAAGCTGGCCTTGCC
CCTGCTCCCATCTTTTCATTTGCCTTCCCTCATGTCTTCCTTACCCACTTTAGCCCTCACCACCTCCCATGTTCCCACCC
CTGCCCCGGAATACCCCCTTTTATCAAGGCCAGCCCTTTCCACCCTGTGAAATCAAATACAATGTAATGGAGGGCTTCTC
AATGCCAGGATATGGCCCTGGAATGGACTTTGTGCCTGGTCTCCTGCCACCATCAATCTCTGGCCCTGTCTCCCATGCTC
AACACCGGGGCCCAGTGGTCCACTGAAGCAAGCCATGTTGTGTTCTGAACAACCTCTACCATGTACCATGGATCGGGGAC
CCATGCAGGCATCGACTTAGACATTCAGACAGACTGATCCACACATATAAACAGGACAGACGGGGGCATGCCCATTTGGG
AACATGGCCTGGA

Alignment

ORF - retro_mmus_1001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.35 %
• Parental protein coverage: 85.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KGELSFEQDQLVAGGQLGELHNGTQYREVRQFCSGSGHHLVRFYFLTRV-YSEYLEDILEELSYGPAPDL
          .GELSF.QDQLVAGGQLGE..NG..Y..VRQFCSGS.H..V.FYFLTRV.YSEYLED.LEEL.YGP.PDL
Retrocopy QGELSFAQDQLVAGGQLGERRNGK*YCQVRQFCSGSDHYFVCFYFLTRV<YSEYLEDFLEEL*YGPSPDL

Parental  VIINSCLWDLSRYGRCSMESYRENLERVFVRMDQVLPDSCLLVWNLAMPLGER-VTGGFLLP-ELQPLAV
          VIINS.LWDLSRYGRCS.ES.RENLER.FVRMD.VLPDSCLLVWNLA...GE..VTGGF.LP..LQPLAV
Retrocopy VIINS*LWDLSRYGRCSIESFRENLERAFVRMDHVLPDSCLLVWNLAISFGET>VTGGFFLP<RLQPLAV

Parental  SLRQDVVEGNFYSATLAGKHCFDVLDLHFHFRHA-VRHRHRDGVHWDQHAHRHLSHLLLAHVADAWGVEL
          SL.QDVVE.NFY.ATLAG..CF.VLDL.F.F.H..V.HRHRD.VHWDQHAHRHLSHLLL.H....W.VE.
Retrocopy SLLQDVVERNFYKATLAGNYCFVVLDLQFRFQHC>VHHRHRDCVHWDQHAHRHLSHLLLTH----WAVEP

Parental  PKHDRLPDPWIEDWSEMDHSFQGSH-KQPPDFREKLALPLLPPFHLPPPMS-FPYPLEPSPPPLFPPLP-
          PKH..LPD.W.E.W.EMDHSFQGSH.KQPPDFREKLALPLLP.FHLP..MS.F.....P...P...P.P.
Retrocopy PKHGHLPDLWVEVWPEMDHSFQGSH>KQPPDFREKLALPLLPSFHLPSLMS<FLTHFSPHHLPCSHPCP<

Parental  QDTPFFQGQPFPPYEFKYNAMEDFSMPGCGPGMNFVPGPLPPSVSGPVSHGQHRGPVVHRGKPRCVLNNP
          ..TPF.QGQPFPP.E.KYN.ME.FSMPG.GPGM.FVPG.LPPS.SGPVSH.QHRGPVVH..KP.CVLNN.
Retrocopy RNTPFYQGQPFPPCEIKYNVMEGFSMPGYGPGMDFVPGLLPPSISGPVSHAQHRGPVVH*SKPCCVLNNL

Parental  YHVPRIGGPCRHRLRHSDRLIHTYKQDRRGHAHSGTWPG
          YHVP.IG.PCRHRLRHSDRLIHTYKQDRRGHAH.GTWPG
Retrocopy YHVPWIGDPCRHRLRHSDRLIHTYKQDRRGHAHLGTWPG

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	0.04 RPM	15.94 RPM
SRP007412_heart	0.03 RPM	9.09 RPM
SRP007412_kidney	0.02 RPM	12.07 RPM
SRP007412_liver	0.03 RPM	13.30 RPM
SRP007412_testis	0.05 RPM	29.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1001 was not detected

EST

No EST(s) were mapped for retro_mmus_1001 retrocopy.

TSS

No TSS is located nearby retro_mmus_1001 retrocopy 5' end.

Lab

retro_mmus_1001 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1001 has 0 orthologous retrocopies within eutheria group .

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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,