RetrogeneDB ID: retro_mmus_2399

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:143389658..143390156(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081792
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Anp32b
• Ensembl ID: ENSMUSG00000028333
• Aliases: Anp32b, 2410015B15Rik, PAL31, PHAPI2a, Ssp29
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member B [Source:MGI Symbol;Acc:MGI:1914878]

Sequence

>retro_mmus_2399
ATGGATATGAAGAGGAGGATCCACCTGGAGCTGAGGAACCGGACCCCGGCAGCCGTTCGAGAACTTGTCTTGGACAATTG
CAAAGCAATGGATGGAAAAATGGAGGGGTTAACAGATGAATTTGTGAACTTAGAGTTCCTCAGTTTAATAAGTGTAGGCT
TGTTTTCAGTTTCAGACCTCCCGAAGCTACCTAAATTGAAGAAGCTTGAGCTCAGTGAAAATAGAATCTTCGGAGGTCTG
GACAGACTAGCAGAAGAACTTCCAAGCCTCACACATCTGAACCCAAGTGGAAATAACCTGAAAGATATCAGCACCTTGGA
GCCGTTGAAAAGGTTGGATTGTCTGAAAAGCCTGGATCTGTTTGGCTGTGAGGTCACTAACCAGAGTGATTACCGAGAAA
CTGTCTTCAGGCTCCTGCCCCAGCTGTCCTATCTGGATGGCTATGACCGAGAGGACCAGGAAGCCCCCGACTCAGATGTG
GAGGTGGATGGTGTGGAC

Alignment

ORF - retro_mmus_2399 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.99 %
• Parental protein coverage: 61.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDMKRRIHLELRNRTPAAVRELVLDNCKAMDGKIEGLTDEFVNLEFLSLISVGLFSVSDLPKLPKLKKLE
          MDMKRRIHLELRNRTPAAVRELVLDNCKAMDGK.EGLTDEFVNLEFLSLISVGLFSVSDLPKLPKLKKLE
Retrocopy MDMKRRIHLELRNRTPAAVRELVLDNCKAMDGKMEGLTDEFVNLEFLSLISVGLFSVSDLPKLPKLKKLE

Parental  LSENRIFGGLDRLAEELPSLTHLNLSGNNLKDISTLEPLKRLDCLKSLDLFGCEVTNRSDYRETVFRLLP
          LSENRIFGGLDRLAEELPSLTHLN.SGNNLKDISTLEPLKRLDCLKSLDLFGCEVTN.SDYRETVFRLLP
Retrocopy LSENRIFGGLDRLAEELPSLTHLNPSGNNLKDISTLEPLKRLDCLKSLDLFGCEVTNQSDYRETVFRLLP

Parental  QLSYLDGYDREDQEAPDSDVEVDSVE
          QLSYLDGYDREDQEAPDSDVEVD.V.
Retrocopy QLSYLDGYDREDQEAPDSDVEVDGVD

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	0.02 RPM	29.86 RPM
SRP007412_cerebellum	0.00 RPM	50.89 RPM
SRP007412_heart	0.03 RPM	51.49 RPM
SRP007412_kidney	0.06 RPM	78.40 RPM
SRP007412_liver	0.03 RPM	47.82 RPM
SRP007412_testis	0.00 RPM	75.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2399 was not detected

EST

No EST(s) were mapped for retro_mmus_2399 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_102683	226 libraries	402 libraries	430 libraries	10 libraries	4 libraries

The graphical summary, for retro_mmus_2399 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_2399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2399 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005149	6 retrocopies	retro_chof_1293, retro_chof_1456, retro_chof_19, retro_chof_2244, retro_chof_588, retro_chof_681,
Cavia porcellus	ENSCPOG00000020118	3 retrocopies	retro_cpor_1336, retro_cpor_493, retro_cpor_509,
Equus caballus	ENSECAG00000012310	2 retrocopies	retro_ecab_246, retro_ecab_826,
Echinops telfairi	ENSETEG00000015514	4 retrocopies	retro_etel_2053, retro_etel_2167, retro_etel_510, retro_etel_677,
Homo sapiens	ENSG00000136938	2 retrocopies	retro_hsap_1597, retro_hsap_1603,
Myotis lucifugus	ENSMLUG00000004844	2 retrocopies	retro_mluc_1787, retro_mluc_1788,
Macaca mulatta	ENSMMUG00000012242	1 retrocopy	retro_mmul_2600,
Monodelphis domestica	ENSMODG00000003261	1 retrocopy	retro_mdom_763,
Mustela putorius furo	ENSMPUG00000006433	1 retrocopy	retro_mputfur_1392,
Mus musculus	ENSMUSG00000028333	1 retrocopy	retro_mmus_2399 ,
Nomascus leucogenys	ENSNLEG00000016941	1 retrocopy	retro_nleu_3009,
Otolemur garnettii	ENSOGAG00000006091	2 retrocopies	retro_ogar_1915, retro_ogar_3282,
Pongo abelii	ENSPPYG00000019430	2 retrocopies	retro_pabe_1312, retro_pabe_1316,
Pan troglodytes	ENSPTRG00000021172	3 retrocopies	retro_ptro_1073, retro_ptro_1075, retro_ptro_40,
Pteropus vampyrus	ENSPVAG00000006569	1 retrocopy	retro_pvam_699,
Sorex araneus	ENSSARG00000000804	1 retrocopy	retro_sara_549,
Tupaia belangeri	ENSTBEG00000002189	8 retrocopies	retro_tbel_1659, retro_tbel_2710, retro_tbel_2772, retro_tbel_3770, retro_tbel_3863, retro_tbel_4351, retro_tbel_4361, retro_tbel_491,
Tursiops truncatus	ENSTTRG00000010825	2 retrocopies	retro_ttru_1899, retro_ttru_341,