RetrogeneDB ID: retro_mmus_2545

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:8971947..8972139(+)
• Located in intron of: ENSMUSG00000003623

Retrocopy information

• Ensembl ID: ENSMUSG00000078183
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tma7
• Ensembl ID: ENSMUSG00000091537
• Aliases: Tma7, 1110017O22Rik, Ccdc72
• Description: translational machinery associated 7 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913417]

Sequence

>retro_mmus_2545
ATGTCGGGCTGGGAAGGTGGCAAAAAGAAGCCCCTGAAACAGCCCAAGAAGCAGGCCAAGGAGATGGACGAGGAAGATAA
GGCTTTCAAGCAGAATCAAAAGGAGGAACGGAAGAAACTCGAGGAGCTAAAAGCCAAGGCCGCCGGGAAGGGCCCCCTGG
CCACAGGTGGAATTAAGAAATCTGGCAAAAAG

Alignment

ORF - retro_mmus_2545 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGREGGKKKPLKQPKKQAKEMDEEDKAFKQKQKEEQKKLEELKAKAAGKGPLATGGIKKSGKK
          MSG.EGGKKKPLKQPKKQAKEMDEEDKAFKQ.QKEE.KKLEELKAKAAGKGPLATGGIKKSGKK
Retrocopy MSGWEGGKKKPLKQPKKQAKEMDEEDKAFKQNQKEERKKLEELKAKAAGKGPLATGGIKKSGKK

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	0.12 RPM	10.07 RPM
SRP007412_cerebellum	0.17 RPM	7.08 RPM
SRP007412_heart	0.00 RPM	17.53 RPM
SRP007412_kidney	0.33 RPM	15.34 RPM
SRP007412_liver	0.25 RPM	11.03 RPM
SRP007412_testis	0.69 RPM	15.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2545 was not detected

EST

No EST(s) were mapped for retro_mmus_2545 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_116072	532 libraries	238 libraries	276 libraries	24 libraries	2 libraries

The graphical summary, for retro_mmus_2545 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_2545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2545 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001193	6 retrocopies	retro_amel_1070, retro_amel_1643, retro_amel_270, retro_amel_503, retro_amel_826, retro_amel_879,
Callithrix jacchus	ENSCJAG00000002871	18 retrocopies	retro_cjac_1370, retro_cjac_1449, retro_cjac_1504, retro_cjac_1667, retro_cjac_1670, retro_cjac_1704, retro_cjac_1918, retro_cjac_2092, retro_cjac_2258, retro_cjac_2422, retro_cjac_2629, retro_cjac_2673, retro_cjac_2692, retro_cjac_2799, retro_cjac_3651, retro_cjac_536, retro_cjac_81, retro_cjac_849,
Felis catus	ENSFCAG00000026902	5 retrocopies	retro_fcat_138, retro_fcat_1630, retro_fcat_173, retro_fcat_57, retro_fcat_630,
Gorilla gorilla	ENSGGOG00000028044	3 retrocopies	retro_ggor_11, retro_ggor_2002, retro_ggor_209,
Mus musculus	ENSMUSG00000091537	11 retrocopies	retro_mmus_1216, retro_mmus_1582, retro_mmus_1632, retro_mmus_2117, retro_mmus_2189, retro_mmus_2222, retro_mmus_2545 , retro_mmus_2975, retro_mmus_3235, retro_mmus_389, retro_mmus_412,
Pan troglodytes	ENSPTRG00000041769	9 retrocopies	retro_ptro_136, retro_ptro_1492, retro_ptro_150, retro_ptro_1638, retro_ptro_1953, retro_ptro_1976, retro_ptro_2312, retro_ptro_2535, retro_ptro_2691,
Rattus norvegicus	ENSRNOG00000042689	2 retrocopies	retro_rnor_316, retro_rnor_894,
Rattus norvegicus	ENSRNOG00000047225	1 retrocopy	retro_rnor_1709,
Sus scrofa	ENSSSCG00000011351	6 retrocopies	retro_sscr_133, retro_sscr_19, retro_sscr_299, retro_sscr_541, retro_sscr_735, retro_sscr_910,