RetrogeneDB ID: retro_mmus_2539

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:155502320..155502705(-)
• Located in intron of: ENSMUSG00000029064

Retrocopy information

• Ensembl ID: ENSMUSG00000082429
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufb7
• Ensembl ID: ENSMUSG00000033938
• Aliases: Ndufb7, 1110002H15Rik
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7 [Source:MGI Symbol;Acc:MGI:1914166]

Sequence

>retro_mmus_2539
CGGGTGCTGTGGGATGCCTCGGTGGAGCCTGACCTGGAGAAGACGCCCAGCTTCCCAACGGACCTCGGCTTCCCGAAGCG
CAAGGAGCGAGTGACGGTAGCCACACAACAAGAGATAATGGATGCCCAGGTGACACTGCAGCGACGTGACTACTGTGCCC
ACTACCTACCCAGCTGCTGAAATGCAACAGAGACAGCTTGCCAGGTTCCTGGCCTGCAAGCGTGAGCAGCACAGCTGGGA
CTACTGCGAGCACCTGGACTACGTGAAGCACATGAAGGAATTTGAACGTGAGCAGCGACTGCTCCAAAGGAAGAAGCGGA
GGGCACTGAAGGAAGCACGGGTAGCCCAAGGCCAGGGAGATGGAGAGGTGGGCCCTGAGGTGGCC

Alignment

ORF - retro_mmus_2539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.97 %
• Parental protein coverage: 94.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RYLWDASVEPDPEKIPSFPPDLGFPERKERVMVATQQEMMDAQLTLQQRDYCAHYL-IRLLKCKRDSFPN
          R.LWDASVEPD.EK.PSFP.DLGFP.RKERV.VATQQE.MDAQ.TLQ.RDYCAHYL...LLKC.RDS.P.
Retrocopy RVLWDASVEPDLEKTPSFPTDLGFPKRKERVTVATQQEIMDAQVTLQRRDYCAHYL<TQLLKCNRDSLPG

Parental  -FLACKHEQHDWDYCEHLDYVKRMKEFERERRLLQRKKRRALKEARVAQGQGEGEVGPEVA
          .FLACK.EQH.WDYCEHLDYVK.MKEFERE.RLLQRKKRRALKEARVAQGQG.GEVGPEVA
Retrocopy <FLACKREQHSWDYCEHLDYVKHMKEFEREQRLLQRKKRRALKEARVAQGQGDGEVGPEVA

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	0.05 RPM	40.07 RPM
SRP007412_cerebellum	0.00 RPM	54.45 RPM
SRP007412_heart	0.03 RPM	204.59 RPM
SRP007412_kidney	0.10 RPM	122.76 RPM
SRP007412_liver	0.03 RPM	56.26 RPM
SRP007412_testis	0.09 RPM	48.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2539 was not detected

EST

No EST(s) were mapped for retro_mmus_2539 retrocopy.

TSS

No TSS is located nearby retro_mmus_2539 retrocopy 5' end.

Lab

retro_mmus_2539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2539 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011470	1 retrocopy	retro_amel_1288,
Canis familiaris	ENSCAFG00000016258	1 retrocopy	retro_cfam_1718,
Dipodomys ordii	ENSDORG00000015213	1 retrocopy	retro_dord_6,
Mus musculus	ENSMUSG00000033938	1 retrocopy	retro_mmus_2539 ,
Otolemur garnettii	ENSOGAG00000009615	1 retrocopy	retro_ogar_2154,