RetrogeneDB ID: retro_mmus_1201

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:51579730..51580264(+)
• Located in intron of: ENSMUSG00000079244

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nudt4
• Ensembl ID: ENSMUSG00000020029
• Aliases: Nudt4, 4933436C10Rik, DIPP2, DIPP2alpha, DIPP2beta, HDCMB47P
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 4 [Source:MGI Symbol;Acc:MGI:1918457]

Sequence

>retro_mmus_1201
ATGAAGTTCAAGCCCAAGCAGACACTGACATAAACCCTGAAGGGCTTCAATAATGAACAGCCTGCCTGTGCTTCCACAGC
AAGCAGGAGGAAGAGGGGCCTTTGGTGAGTAGCAGTAGTCCCCAGAGCAATGCATTGTCCCAGGAGGAGGGTTGGAGACA
GAGTAGGAGCCTGGCTTTGCTGCTGTGAGGGAGGTTTATGAAGAGGCTGGAAGGAAAGAAAAATTAGGCAGACTCCTGGG
AATATTTGAGCAGACTCAACACTGGAAGCACAGAACATATGTTCATGTTCTAACAGTCACTGAAATATTGGAAGGCTGGG
AAGACTCTGTGACTATAGGAAGGAAGAGAGAATGGTTCAAAGGAGATGTAATCAAGGTTCTTCAGTGACATTAGCCTGTC
CACACAGAGTATCCAAAAAACTAAAGCTGGGGTGTTCTCCAACCAATGGACAGTCCAGGGTCCCTTCCCTCCCAGATAGC
AATGCCTTGTTTGTGACTGCTGTACAGCCCTCTGGGGTACCTTCCAGTATAAAG

Alignment

ORF - retro_mmus_1201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKFKPNQTRTYDREGFKKR-AACLCFRSEQEDEVLLVSSSR-YPDQWIVPGGGMEPEEEPGGAAVREVYE
          MKFKP.QT.T....GF.....ACLCF.S.QE.E..LVSSS...P.Q.IVPGGG.E.E.EPG.AAVREVYE
Retrocopy MKFKPKQTLT*TLKGFNNE<TACLCFHSKQEEEGPLVSSSS<SPEQCIVPGGGLETE*EPGFAAVREVYE

Parental  EAGVKGKLGRLLGIFEN-QDRKHRTYVYVLTVTEILEDWEDSVNIGRKREWFKVEDAIKVLQCHKPVHAE
          EAG.K.KLGRLLGIFE..Q..KHRTYV.VLTVTEILE.WEDSV.IGRKREWFK..D.IKVLQ.H.PVH.E
Retrocopy EAGRKEKLGRLLGIFEQTQHWKHRTYVHVLTVTEILEGWEDSVTIGRKREWFK-GDVIKVLQ*H*PVHTE

Parental  Y-LEKLKLGCSPTNGNSSVPSLPDNNALFVTAAPPSGVPSSIR
          Y...KLKLGCSPTNG.S.VPSLPD.NALFVTA..PSGVPSSI.
Retrocopy Y<SKKLKLGCSPTNGQSRVPSLPDSNALFVTAVQPSGVPSSIK

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	123.03 RPM
SRP007412_cerebellum	0.00 RPM	85.06 RPM
SRP007412_heart	0.00 RPM	180.21 RPM
SRP007412_kidney	0.00 RPM	462.55 RPM
SRP007412_liver	0.00 RPM	118.11 RPM
SRP007412_testis	0.00 RPM	647.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1201 was not detected

EST

No EST(s) were mapped for retro_mmus_1201 retrocopy.

TSS

No TSS is located nearby retro_mmus_1201 retrocopy 5' end.

Lab

retro_mmus_1201 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1201 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009844	2 retrocopies	retro_amel_1401, retro_amel_36,
Dasypus novemcinctus	ENSDNOG00000015207	3 retrocopies	retro_dnov_1906, retro_dnov_2555, retro_dnov_41,
Dipodomys ordii	ENSDORG00000000647	3 retrocopies	retro_dord_26, retro_dord_272, retro_dord_660,
Equus caballus	ENSECAG00000019319	1 retrocopy	retro_ecab_472,
Echinops telfairi	ENSETEG00000013922	2 retrocopies	retro_etel_1627, retro_etel_2111,
	ENSG00000173598	0 retrocopies
Gorilla gorilla	ENSGGOG00000014324	1 retrocopy	retro_ggor_108,
Loxodonta africana	ENSLAFG00000013776	1 retrocopy	retro_lafr_1131,
Microcebus murinus	ENSMICG00000007100	2 retrocopies	retro_mmur_1521, retro_mmur_1565,
Myotis lucifugus	ENSMLUG00000002767	1 retrocopy	retro_mluc_753,
Monodelphis domestica	ENSMODG00000009468	1 retrocopy	retro_mdom_214,
Mus musculus	ENSMUSG00000020029	3 retrocopies	retro_mmus_1201 , retro_mmus_1202, retro_mmus_1203,
Oryctolagus cuniculus	ENSOCUG00000011283	1 retrocopy	retro_ocun_1905,
Pteropus vampyrus	ENSPVAG00000013730	1 retrocopy	retro_pvam_1423,
Ictidomys tridecemlineatus	ENSSTOG00000020306	1 retrocopy	retro_itri_112,
Tupaia belangeri	ENSTBEG00000012198	7 retrocopies	retro_tbel_1705, retro_tbel_2322, retro_tbel_3443, retro_tbel_3472, retro_tbel_3733, retro_tbel_3739, retro_tbel_4678,
Tursiops truncatus	ENSTTRG00000003309	2 retrocopies	retro_ttru_1625, retro_ttru_1925,
Vicugna pacos	ENSVPAG00000002957	1 retrocopy	retro_vpac_507,