RetrogeneDB ID: retro_mmus_1773

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:45418658..45419153(-)
• Located in intron of: ENSMUSG00000054477

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc53
• Ensembl ID: ENSMUSG00000020056
• Aliases: Ccdc53, 2900091E11Rik, 5730495F03Rik
• Description: coiled-coil domain containing 53 [Source:MGI Symbol;Acc:MGI:1914532]

Sequence

>retro_mmus_1773
ATAGATGAGGGTGGGTTTCCTCTTATGGGGTCAGGCATAACCAAGGTGCCAGATAGTTAGTGGAAAAGAACCGTGGCATT
TCTAAGCCAGTTGTCACATGTACTGTGCAGTTTTCTCGACGTTTTCCACAGTTTGTGAGGAGAACCTGGCATACCTTTCT
CTTTGTGTTCAAAGAAATTAAAACAAACTCTCAATATTTTAGACTCTCAATGTGAAGCTGTCATCTACCCCAGGCCTAGA
GGAGGTCACAGTTGAAGTGTCTCCTTTAAATGTCAGTGCTGTCACAAATGGATCACCATTCTGAAACCACTTCAGATCAA
CCACATCACAACAGTACACGAGACTCTCAGCCACAGGAAAATGAGGCATCATCAGAAAGTATCTTGAATGTCGTCACAAA
TTCAAGATATCCCAGGTATCTCAAGATGGTCCCAATGACAGCAATCAAAGACAAAATGGTATCAGGGCTGGGTCCCAGAG
CTCCCTGAGAAGCCC

Alignment

ORF - retro_mmus_1773 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 87.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDEDGLPLMGSGIDLTKVPAIQQKRTVAFLNQF-VVHTVQFLNRF-SAVCEEKLADLSLRIQQIETTLNI
          .DE.G.PLMGSGI..TKVP....KRTVAFL.Q..V..TVQF..RF.S.VCEE.LA.LSL..Q.....L.I
Retrocopy IDEGGFPLMGSGI--TKVPDS*WKRTVAFLSQL<VTCTVQFSRRF<STVCEENLAYLSLCVQRN*NKLSI

Parental  ---LDAKLSSIPGLEDVTVEVSPLNVTAVTNGS-HSETTSEQTQQNSTQDSGAQESEAPSENVLTVAKDP
          ...L..KLSS.PGLE.VTVEVSPLNV.AVTNGS.HSETTS.Q...NST.DS..QE.EA.SE..L.V....
Retrocopy F*TLNVKLSSTPGLEEVTVEVSPLNVSAVTNGS>HSETTSDQPHHNSTRDSQPQENEASSESILNVVTNS

Parental  RYARYLKMVQVGVPVMAIRDKMISEGLD-PELLEKP
          RY.RYLKMV....P..AI.DKM.S.GL..PEL.EKP
Retrocopy RYPRYLKMV----PMTAIKDKMVS-GLG>PELPEKP

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	7.31 RPM
SRP007412_cerebellum	0.00 RPM	5.47 RPM
SRP007412_heart	0.00 RPM	7.47 RPM
SRP007412_kidney	0.00 RPM	12.36 RPM
SRP007412_liver	0.00 RPM	9.86 RPM
SRP007412_testis	0.00 RPM	23.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1773 was not detected

EST

No EST(s) were mapped for retro_mmus_1773 retrocopy.

TSS

No TSS is located nearby retro_mmus_1773 retrocopy 5' end.

Lab

retro_mmus_1773 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1773 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006329	1 retrocopy	retro_amel_791,
Canis familiaris	ENSCAFG00000007270	2 retrocopies	retro_cfam_53, retro_cfam_550,
Callithrix jacchus	ENSCJAG00000014225	1 retrocopy	retro_cjac_4073,
Echinops telfairi	ENSETEG00000002254	1 retrocopy	retro_etel_1917,
Felis catus	ENSFCAG00000019358	1 retrocopy	retro_fcat_498,
Homo sapiens	ENSG00000120860	1 retrocopy	retro_hsap_4696,
Gorilla gorilla	ENSGGOG00000014975	1 retrocopy	retro_ggor_2922,
Loxodonta africana	ENSLAFG00000007850	1 retrocopy	retro_lafr_761,
Macropus eugenii	ENSMEUG00000004888	3 retrocopies	retro_meug_1441, retro_meug_576, retro_meug_629,
Myotis lucifugus	ENSMLUG00000000401	4 retrocopies	retro_mluc_2014, retro_mluc_2015, retro_mluc_2633, retro_mluc_502,
Monodelphis domestica	ENSMODG00000002579	1 retrocopy	retro_mdom_959,
Mus musculus	ENSMUSG00000020056	1 retrocopy	retro_mmus_1773 ,
Nomascus leucogenys	ENSNLEG00000006365	1 retrocopy	retro_nleu_2366,
Otolemur garnettii	ENSOGAG00000003322	2 retrocopies	retro_ogar_3267, retro_ogar_738,
Pongo abelii	ENSPPYG00000004878	1 retrocopy	retro_pabe_3649,
Pan troglodytes	ENSPTRG00000005358	1 retrocopy	retro_ptro_3121,
Ictidomys tridecemlineatus	ENSSTOG00000001870	1 retrocopy	retro_itri_970,
Tupaia belangeri	ENSTBEG00000008498	3 retrocopies	retro_tbel_1036, retro_tbel_1165, retro_tbel_2967,
Tarsius syrichta	ENSTSYG00000000587	4 retrocopies	retro_tsyr_1100, retro_tsyr_265, retro_tsyr_443, retro_tsyr_955,
Tursiops truncatus	ENSTTRG00000017221	4 retrocopies	retro_ttru_1569, retro_ttru_1865, retro_ttru_1919, retro_ttru_935,
Vicugna pacos	ENSVPAG00000002010	1 retrocopy	retro_vpac_446,