RetrogeneDB ID: retro_mmus_2284

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:104417614..104418271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pdcl3
• Ensembl ID: ENSMUSG00000026078
• Aliases: Pdcl3, 1110061A19Rik, C80025, Viaf1
• Description: phosducin-like 3 [Source:MGI Symbol;Acc:MGI:1916083]

Sequence

>retro_mmus_2284
CCTTCTACAGAGAGCCGGAAGAAGCTGGAGGAGGAAGAAATGGAGAAGGAGGAGCAGCTCCTTCAGCAGTTAGTAGTGAA
ATCATACGAAGACACGACTCTGGAAGAGCTGGAGGAGAAGGAGCGTGAGCTCAGAGATGAGGACGAACGAGCTGTTGAGA
TATACCAAAGGGTGCCTGAGTGGAAAAGCAACTCAACTGAAGAACAAATTTGGAGAAGTTTTAGAGATCTCAGGAAAGGA
CTATGTTCAAGAAGTTACGAAAGCTGGCGAGGGCTTGTGGGTGGTCTTACACCTATACAAAAAAGGGATTCCCCTCTGTT
CCTTGATAAACTATCGCTTGAGTGGATTCGCTAAGAAGTTTCCAGATGTGAAATTTATCAAAGCCATTTTAACGACCTGC
ATACCCAACTACCCCAACAGGAATCTCCCCACAGTGTTCGTCTACCAGGAAGGGGATCTCAAGGCACAGTTCTTCGGTCC
TCTGGTGTTCGGTGGCGTGAACCTGACCATGGATGAGTTGGAGTGGAAGCTGTCTTGAGTCCGGAGCAATCAAGACAGAC
TTGGAGGAGAACCTCCAAAGAACCCATTCAAGACCTGCTGCTGTCCTCAGTACGGGGCCCTGTCCCCATGAGGAGGGACA
GTGATTCCAAGGGTGAC

Alignment

ORF - retro_mmus_2284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.06 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PPKESLKELEEEEAEKEEQLLQQSVVKTYEDMTLEELEENEDEFSEEDERAIEMYRQQRLAEW-KATQLK
          P..ES.K.LEEEE.EKEEQLLQQ.VVK.YED.TLEELEE.E.E...EDERA.E.Y..QR..EW.KATQLK
Retrocopy PSTESRKKLEEEEMEKEEQLLQQLVVKSYEDTTLEELEEKERELRDEDERAVEIY--QRVPEW>KATQLK

Parental  NKFGEVLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCSLINHHLSGLARKFPDVKFIKAISTTCIPNY
          NKFGEVLEISGKDYVQEVTKAGEGLWV.LHLYK.GIPLCSLIN..LSG.A.KFPDVKFIKAI.TTCIPNY
Retrocopy NKFGEVLEISGKDYVQEVTKAGEGLWVVLHLYKKGIPLCSLINYRLSGFAKKFPDVKFIKAILTTCIPNY

Parental  PDRNLPTVFVYREGDIKAQFIGPLVFGGMNLTIDELEWKLS-ESGAIKTALEEN-PKKPIQDLLLSSVRG
          P.RNLPTVFVY.EGD.KAQF.GPLVFGG.NLT.DELEWKLS.ESGAIKT.LEEN..K.PIQDLLLSSVRG
Retrocopy PNRNLPTVFVYQEGDLKAQFFGPLVFGGVNLTMDELEWKLS>ESGAIKTDLEEN>SKEPIQDLLLSSVRG

Parental  PVPMRRDSDSEDD
          PVPMRRDSDS..D
Retrocopy PVPMRRDSDSKGD

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	0.02 RPM	18.08 RPM
SRP007412_cerebellum	0.00 RPM	30.00 RPM
SRP007412_heart	0.00 RPM	52.55 RPM
SRP007412_kidney	0.00 RPM	50.38 RPM
SRP007412_liver	0.00 RPM	18.13 RPM
SRP007412_testis	0.41 RPM	6.40 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2284 was not detected

EST

No EST(s) were mapped for retro_mmus_2284 retrocopy.

TSS

No TSS is located nearby retro_mmus_2284 retrocopy 5' end.

Lab

retro_mmus_2284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2284 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002226	1 retrocopy	retro_cfam_1740,
Callithrix jacchus	ENSCJAG00000010160	3 retrocopies	retro_cjac_1486, retro_cjac_1599, retro_cjac_2055,
Dipodomys ordii	ENSDORG00000012397	1 retrocopy	retro_dord_702,
Erinaceus europaeus	ENSEEUG00000000224	1 retrocopy	retro_eeur_506,
Homo sapiens	ENSG00000115539	7 retrocopies	retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535, retro_hsap_3961, retro_hsap_4102,
Myotis lucifugus	ENSMLUG00000016446	1 retrocopy	retro_mluc_1443,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734,
Mus musculus	ENSMUSG00000026078	1 retrocopy	retro_mmus_2284 ,
Nomascus leucogenys	ENSNLEG00000014393	8 retrocopies	retro_nleu_1499, retro_nleu_1575, retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus	ENSOCUG00000001469	2 retrocopies	retro_ocun_1035, retro_ocun_920,
Otolemur garnettii	ENSOGAG00000015138	2 retrocopies	retro_ogar_1147, retro_ogar_2959,
Ochotona princeps	ENSOPRG00000011600	2 retrocopies	retro_opri_1070, retro_opri_289,
Tursiops truncatus	ENSTTRG00000006242	1 retrocopy	retro_ttru_1184,