RetrogeneDB ID: retro_mmus_1930

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:68831016..68831256(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082836
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H2-Ke2
• Ensembl ID: ENSMUSG00000024309
• Aliases: H2-Ke2, H-2Ke2, Ke-2, Pfdn6
• Description: H2-K region expressed gene 2 [Source:MGI Symbol;Acc:MGI:95908]

Sequence

>retro_mmus_1930
ATGGCTGAACTGATCCAAAAGAAGCTGCAGGGAGAGGTAGAGAAATATCAACAGCTGCAGAAGGACTTGAGTAAATCTAT
GTCAGGGAGGCAGAAGCTCGAAGCACAGCTAAGGGAAAACAATATCCTGAAGGAGGAGCTGGCCCTGCTGGATGGATCCA
AAGTAGTCTTTAAGCTTCTGGGACCCGTGCTAGTCAAAGAGGAGCTGGGGGAGGCTCGGGCCACGGTGGGGAAGAGGCTA

Alignment

ORF - retro_mmus_1930 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.0 %
• Parental protein coverage: 62.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG
          MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQL.ENNI.KEELALLDGS.VVFKLLGPVLVK.ELG
Retrocopy MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLRENNILKEELALLDGSKVVFKLLGPVLVKEELG

Parental  EARATVGKRL
          EARATVGKRL
Retrocopy EARATVGKRL

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	21.26 RPM
SRP007412_cerebellum	0.00 RPM	29.57 RPM
SRP007412_heart	0.00 RPM	28.70 RPM
SRP007412_kidney	0.02 RPM	25.04 RPM
SRP007412_liver	0.05 RPM	20.29 RPM
SRP007412_testis	0.00 RPM	44.92 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1930 was not detected

EST

No EST(s) were mapped for retro_mmus_1930 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_88299	461 libraries	351 libraries	249 libraries	10 libraries	1 library

The graphical summary, for retro_mmus_1930 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_1930 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1930 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Cavia porcellus	ENSCPOG00000019520	1 retrocopy	retro_cpor_570,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mus musculus	ENSMUSG00000024309	1 retrocopy	retro_mmus_1930 ,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Rattus norvegicus	ENSRNOG00000000473	2 retrocopies	retro_rnor_2216, retro_rnor_2869,
Sorex araneus	ENSSARG00000006330	2 retrocopies	retro_sara_338, retro_sara_453,
Tupaia belangeri	ENSTBEG00000013280	1 retrocopy	retro_tbel_454,