RetrogeneDB ID: retro_mmus_2537

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:150315179..150315437(-)
• Located in intron of: ENSMUSG00000039852

Retrocopy information

• Ensembl ID: ENSMUSG00000085787
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Snrpf
• Ensembl ID: ENSMUSG00000020018
• Aliases: Snrpf, 2010013O18Rik, SMF, sm-F, snRNP-F
• Description: small nuclear ribonucleoprotein polypeptide F [Source:MGI Symbol;Acc:MGI:1917128]

Sequence

>retro_mmus_2537
ATCAGTCTACCCCTCAACCCCAAGCCTTTTCTCAGTGGACTGACAGGGAAGCCAGTGATGGTGAAACTTAAGTGGGGCAT
GGAGTACAAGGGCTACCTGGTCTCCGTGGATGGCTACATGAACATGCAGCTTGCAAATACAGAAGAGTACATAGATGGGG
CGCTGTCTGGACATCTGGGCGAAGTTCTAATAAGGTGTAATAATGTCCTCTACATCAGAGGCGTTGAAGAAGAAGAGGAA
GATGGGGAAATGAGAGAA

Alignment

ORF - retro_mmus_2537 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVL
          .SLPLNPKPFL.GLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVL
Retrocopy ISLPLNPKPFLSGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVL

Parental  YIRGVEEEEEDGEMRE
          YIRGVEEEEEDGEMRE
Retrocopy YIRGVEEEEEDGEMRE

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	0.09 RPM	1.00 RPM
SRP007412_cerebellum	0.04 RPM	1.30 RPM
SRP007412_heart	0.16 RPM	1.00 RPM
SRP007412_kidney	0.10 RPM	0.92 RPM
SRP007412_liver	0.00 RPM	0.52 RPM
SRP007412_testis	0.05 RPM	3.52 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_2537 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	4:150315371..150315560
ENCFF001YKA	POLR2A	4:150315342..150315690

EST

No EST(s) were mapped for retro_mmus_2537 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_103276	61 libraries	185 libraries	257 libraries	39 libraries	530 libraries

The graphical summary, for retro_mmus_2537 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2537 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2537 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Bos taurus	ENSBTAG00000016271	1 retrocopy	retro_btau_765,
Equus caballus	ENSECAG00000019817	1 retrocopy	retro_ecab_154,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Homo sapiens	ENSG00000139343	3 retrocopies	retro_hsap_125, retro_hsap_2487, retro_hsap_2645,
Gorilla gorilla	ENSGGOG00000001127	2 retrocopies	retro_ggor_1549, retro_ggor_225,
Macaca mulatta	ENSMMUG00000009302	4 retrocopies	retro_mmul_1521, retro_mmul_361, retro_mmul_550, retro_mmul_893,
Mustela putorius furo	ENSMPUG00000007176	3 retrocopies	retro_mputfur_1309, retro_mputfur_377, retro_mputfur_941,
Mus musculus	ENSMUSG00000020018	4 retrocopies	retro_mmus_1060, retro_mmus_1197, retro_mmus_2537 , retro_mmus_3210,
Mus musculus	ENSMUSG00000031683	2 retrocopies	retro_mmus_820, retro_mmus_956,
Nomascus leucogenys	ENSNLEG00000005835	3 retrocopies	retro_nleu_2259, retro_nleu_274, retro_nleu_651,
Pongo abelii	ENSPPYG00000004847	2 retrocopies	retro_pabe_381, retro_pabe_489,
Pteropus vampyrus	ENSPVAG00000009036	1 retrocopy	retro_pvam_1170,
Rattus norvegicus	ENSRNOG00000005556	4 retrocopies	retro_rnor_1822, retro_rnor_1849, retro_rnor_2926, retro_rnor_444,
Sus scrofa	ENSSSCG00000000895	1 retrocopy	retro_sscr_958,