RetrogeneDB ID: retro_mmus_3372

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:99220045..99220459(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufs4
• Ensembl ID: ENSMUSG00000021764
• Aliases: Ndufs4, 6720411N02Rik, C1-18k
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 4 [Source:MGI Symbol;Acc:MGI:1343135]

Sequence

>retro_mmus_3372
TCCACATGGAAGCTGGCACAGGATCAAACTGGGGACACACAGCTCGTAACAGTTGATGAGAAATTGGATATCACTACTCT
AACTGGTGTTCCTCGAGAGCACATCAAAACCAGAAAGATCAGCCTCTTTGTTCTTGCTCACAATAACATGCAGCCTGGAG
TAAGCAACACAAAGCATGGAAGATGGTGTTTGATACCAGGGAGAAATGGGAAAAATCCTTGGATGGGTTGGGCATCAACA
GCTGATCCCCTCTCCAACATGGTTCTGACCTTCAGTACCAAAGAAGATGCAATTGTCCTTGCAGGAAAAAAAAATGGATG
GAGCTATGACATGGAAGAGAAGATCCTGAAACCCAAGTCCAAGTCTTGTGGTGCAAACGTTTTTCTGAACAACAGAACAA
GAGTGTCTACAAAA

Alignment

ORF - retro_mmus_3372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.89 %
• Parental protein coverage: 78.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STWKLADNQTRDTQLITVDEKLDITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKK-WKMEFDTRER
          STWKLA..QT.DTQL.TVDEKLDITTLTGVP.EHIKTRK...FV.A.NNMQ.GV.NTK..WKM.FDTRE.
Retrocopy STWKLAQDQTGDTQLVTVDEKLDITTLTGVPREHIKTRKISLFVLAHNNMQPGVSNTKH<WKMVFDTREK

Parental  WE-NPLMGWASTADPLSNMVLTFSAKEDAIAFA-EKNGWSYDVEEKKVPKPKSKSYGANFSWNKRTRVST
          WE.NP.MGWASTADPLSNMVLTFS.KEDAI..A....GWSYD.EE.K..KPKSKS.GAN...N.RTRVST
Retrocopy WE>NPWMGWASTADPLSNMVLTFSTKEDAIVLAXXXXGWSYDMEE-KILKPKSKSCGANVFLNNRTRVST

Parental  K
          K
Retrocopy K

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	38.78 RPM
SRP007412_cerebellum	0.00 RPM	27.01 RPM
SRP007412_heart	0.00 RPM	108.12 RPM
SRP007412_kidney	0.00 RPM	59.37 RPM
SRP007412_liver	0.00 RPM	34.95 RPM
SRP007412_testis	0.00 RPM	26.12 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3372 was not detected

EST

No EST(s) were mapped for retro_mmus_3372 retrocopy.

TSS

No TSS is located nearby retro_mmus_3372 retrocopy 5' end.

Lab

retro_mmus_3372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3372 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005452	1 retrocopy	retro_cpor_1111,
Erinaceus europaeus	ENSEEUG00000015851	3 retrocopies	retro_eeur_133, retro_eeur_30, retro_eeur_347,
Macropus eugenii	ENSMEUG00000001362	1 retrocopy	retro_meug_651,
Monodelphis domestica	ENSMODG00000019465	1 retrocopy	retro_mdom_1227,
Mus musculus	ENSMUSG00000021764	1 retrocopy	retro_mmus_3372 ,
Ochotona princeps	ENSOPRG00000013784	1 retrocopy	retro_opri_508,
Procavia capensis	ENSPCAG00000013496	1 retrocopy	retro_pcap_268,
Pongo abelii	ENSPPYG00000015455	1 retrocopy	retro_pabe_193,
Sus scrofa	ENSSSCG00000016893	1 retrocopy	retro_sscr_999,