RetrogeneDB ID: retro_mmus_317

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:48527605..48527851(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Swi5
• Ensembl ID: ENSMUSG00000044627
• Aliases: Swi5, 1500019F05Rik, 2900010J23Rik, AI046671
• Description: SWI5 recombination repair homolog (yeast) [Source:MGI Symbol;Acc:MGI:1920181]

Sequence

>retro_mmus_317
CCATCTCCCACAACTGAACAGGCTGATGAGATCAAAGAGAAGTCTTTGAACTCTGATATTCAGAAACAGAAGGAGAAGGA
CAGGCTGTATGCACAAGGAGATCTCTCAGATAGCAACTGTGGGTGAACTGGAGGACCGCTTCTCCTTCCTCCATGAATAC
AATGTCATCAAGGATGTAGCACAGATGCTGCTGCACAAGCTGGCATTGTCTCGAGGTGTCACCACAAGGAATTATATCTA
GATTTT

Alignment

ORF - retro_mmus_317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 71.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PFPMIDENNDVSEEALSSDIKKLKEKHDM-LDKEISQLIAEGYRVIELEKHISLLHEYNDIKDVSQMLLG
          P.P.........E..L.SDI.K.KEK......KEISQ....G....ELE...S.LHEYN.IKDV.QMLL.
Retrocopy PSPTTEQADEIKEKSLNSDIQKQKEKDRL>MHKEISQIATVG----ELEDRFSFLHEYNVIKDVAQMLLH

Parental  KLAVTRGVTT-KELYPDF
          KLA..RGVTT.KELY.DF
Retrocopy KLALSRGVTT<KELYLDF

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	67.33 RPM
SRP007412_cerebellum	0.00 RPM	57.58 RPM
SRP007412_heart	0.00 RPM	56.25 RPM
SRP007412_kidney	0.00 RPM	64.83 RPM
SRP007412_liver	0.00 RPM	51.97 RPM
SRP007412_testis	0.00 RPM	129.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_317 was not detected

EST

No EST(s) were mapped for retro_mmus_317 retrocopy.

TSS

No TSS is located nearby retro_mmus_317 retrocopy 5' end.

Lab

retro_mmus_317 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_317 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008548	1 retrocopy	retro_chof_2692,
Mus musculus	ENSMUSG00000044627	2 retrocopies	retro_mmus_317 , retro_mmus_980,
Oryctolagus cuniculus	ENSOCUG00000005318	4 retrocopies	retro_ocun_1628, retro_ocun_1809, retro_ocun_1826, retro_ocun_1836,