RetrogeneDB ID: retro_mmus_459

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:79922538..79923426(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000067106
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Slc25a5
• Ensembl ID: ENSMUSG00000016319
• Aliases: Slc25a5, Ant2
• Description: solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5 [Source:MGI Symbol;Acc:MGI:1353496]

Sequence

>retro_mmus_459
ATGACAGATGCCGCTGTGTCCTTCCCCAAGGACTTCTTGGCCGGTGGAGTGGCCGCAGCCATCTCCAAGATGGCGGTAGC
ACCCATCGAGAGGGTCAAGCTGCTGCTGCAGGTGCAGCATGCCAGCAAGCAAATCATGTCAGATAAGCAATACAAGGGCA
TCATAGACTGCGTGGTTCGTATCCCCAAGGAACAGGGAGTCCTGTACTTCTGGCGTGGGAACCTGGCCAATGACATCAGA
TACTTCCCCACCCAGGCTCTCAACTTTGCCTTCAAAGATAAATACAAGCAGATCTTTCTGGGTGGTGTGGACAAGAGGAC
CCAGTTCTGGCGCTACTTTGCAGGGAACCTGGCATCAGGTGGTGGTGCCGCTGGGGCTACATCCTTGTGCTTTGTGTACC
CTCTTGATTTTGCCCATACCCGTCTAGCAGCTGATGTGGGCAAAGCTGGATCTGAAAAAGGCCTTGGTGACTGCCTGGTT
AAGATCTACAAATCTGATGGGATTAAGGGCCTGTACCAAGGCTTTAATGTGTCAGTACAGGGCATTATCATCTACGGAGC
TGCCTACTTTGGTATCTATGACACTGCAAAGGGAATGCTCCCAGATCCCAAGAATACTCACATCTTCATCAGCTGGATGA
TTGCACAGTTTGTCACTGCTGTCGCTAGCCTGACTTCCTATCCTTTTGACACGGTTCGCCGTCGTATGATGATGCAGTCT
GGACGCAAAGGAACTGATATCATGTACACAGGCACGCTTGACTGCTGGTGGAAGATGGCGCGCGATGAAGGGAGCAAGGC
TTTTTTCAAGGGCACATGGTTCAACGTTCTCAGAGGCATGGGTGGCGCCTTTGTGCTTGTCTTGTACGATGAGATCAAGA
AATACACA

Alignment

ORF - retro_mmus_459 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTDAAVSFAKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQITADKQYKGIIDCVVRIPKEQGVLSF
          MTDAAVSF.KDFLAGGVAAAISK.AVAPIERVKLLLQVQHASKQI..DKQYKGIIDCVVRIPKEQGVL.F
Retrocopy MTDAAVSFPKDFLAGGVAAAISKMAVAPIERVKLLLQVQHASKQIMSDKQYKGIIDCVVRIPKEQGVLYF

Parental  WRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKRTQFWRYFAGNLASGG-AAGATSLCFVYPLDFART
          WRGNLAN.IRYFPTQALNFAFKDKYKQIFLGGVDKRTQFWRYFAGNLASGG.AAGATSLCFVYPLDFA.T
Retrocopy WRGNLANDIRYFPTQALNFAFKDKYKQIFLGGVDKRTQFWRYFAGNLASGGGAAGATSLCFVYPLDFAHT

Parental  RLAADVGKAGAEREFKGLGDCLVKIYKSDGIKGLYQGFNVSVQGIIIYRAAYFGIYDTAKGMLPDPKNTH
          RLAADVGKAG.E...KGLGDCLVKIYKSDGIKGLYQGFNVSVQGIIIY.AAYFGIYDTAKGMLPDPKNTH
Retrocopy RLAADVGKAGSE---KGLGDCLVKIYKSDGIKGLYQGFNVSVQGIIIYGAAYFGIYDTAKGMLPDPKNTH

Parental  IFISWMIAQSVTAVAGLTSYPFDTVRRRMMMQSGRKGTDIMYTGTLDCWRKIARDEGSKAFFKGAWSNVL
          IFISWMIAQ.VTAVA.LTSYPFDTVRRRMMMQSGRKGTDIMYTGTLDCW.K.ARDEGSKAFFKG.W.NVL
Retrocopy IFISWMIAQFVTAVASLTSYPFDTVRRRMMMQSGRKGTDIMYTGTLDCWWKMARDEGSKAFFKGTWFNVL

Parental  RGMGGAFVLVLYDEIKKYT
          RGMGGAFVLVLYDEIKKYT
Retrocopy RGMGGAFVLVLYDEIKKYT

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	108.92 RPM
SRP007412_cerebellum	0.09 RPM	119.06 RPM
SRP007412_heart	0.16 RPM	135.82 RPM
SRP007412_kidney	0.33 RPM	424.44 RPM
SRP007412_liver	0.14 RPM	254.52 RPM
SRP007412_testis	0.00 RPM	17.61 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_459 was not detected

EST

No EST(s) were mapped for retro_mmus_459 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_76659	89 libraries	141 libraries	745 libraries	84 libraries	13 libraries

The graphical summary, for retro_mmus_459 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_459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_459 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000143	1 retrocopy	retro_amel_1291,
Callithrix jacchus	ENSCJAG00000005125	1 retrocopy	retro_cjac_373,
Echinops telfairi	ENSETEG00000004900	2 retrocopies	retro_etel_23, retro_etel_48,
Felis catus	ENSFCAG00000007057	2 retrocopies	retro_fcat_1035, retro_fcat_127,
Gorilla gorilla	ENSGGOG00000014279	8 retrocopies	retro_ggor_1673, retro_ggor_1674, retro_ggor_2146, retro_ggor_2377, retro_ggor_2512, retro_ggor_2517, retro_ggor_2840, retro_ggor_941,
Myotis lucifugus	ENSMLUG00000015742	4 retrocopies	retro_mluc_139, retro_mluc_1580, retro_mluc_2564, retro_mluc_86,
Macaca mulatta	ENSMMUG00000022663	6 retrocopies	retro_mmul_1022, retro_mmul_1287, retro_mmul_1699, retro_mmul_1775, retro_mmul_1800, retro_mmul_2090,
Mus musculus	ENSMUSG00000016319	4 retrocopies	retro_mmus_1173, retro_mmus_1955, retro_mmus_2589, retro_mmus_459 ,
Otolemur garnettii	ENSOGAG00000010008	7 retrocopies	retro_ogar_1131, retro_ogar_1275, retro_ogar_1669, retro_ogar_2161, retro_ogar_2408, retro_ogar_2450, retro_ogar_2474,
Rattus norvegicus	ENSRNOG00000039980	11 retrocopies	retro_rnor_1242, retro_rnor_1364, retro_rnor_1475, retro_rnor_1612, retro_rnor_1904, retro_rnor_1922, retro_rnor_2533, retro_rnor_2758, retro_rnor_721, retro_rnor_722, retro_rnor_723,
Tupaia belangeri	ENSTBEG00000006008	4 retrocopies	retro_tbel_1558, retro_tbel_1860, retro_tbel_4654, retro_tbel_4661,