RetrogeneDB ID: retro_mmus_1857

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:16267063..16267621(-)
• Located in intron of: ENSMUSG00000024639

Retrocopy information

• Ensembl ID: ENSMUSG00000075268
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pebp1
• Ensembl ID: ENSMUSG00000032959
• Aliases: Pebp1, HCNP, Pbp, Pbp1, Pbpr, Rkip
• Description: phosphatidylethanolamine binding protein 1 [Source:MGI Symbol;Acc:MGI:1344408]

Sequence

>retro_mmus_1857
ATGGCCGCCGACATCAGCCAGTGGGCCGGGCCCTTGTGCTTGCAGGAGGTGGACGAGCCGCCCCAGCACGCCCTGCGGGT
CGACTACGCCGGGGTGACGGTGGACGAGCTGGGCAAAGTGCTAACGCCCACCCAGGTTATGAACAGGCCCAGCAGCATTT
CATGGGACGGCCTTGATCCTGGGAAACTCTACACCCTGGTCCTCACAGACCCCGATGCTCCCAGCAGGAAGGATCCCAAA
TTCAGGGAGTGGCACTTCCTGGTGGTCAACATGAAGGGTAACGACATTAGCAGTGGCACTGTCCTCTCAGATTATGTGGG
CTCCGGGCCTCCCAGTGGCACAGGTCTCCACCGCTATGTCTGGCTGGTGTACGAGCAGGAACAGCCGCTGAGCTGCGACG
AGCCCATTCTCAGCAACAAGTCTGGAGACAATCGCGGCAAGTTCAAGGTGGAGACCTTCCGCAAGAAGTATAACCTGGGA
GCCCCGGCGGCGGGCACGTGCTACCAAGCCGAGTGGGATGACTATGTGCCCAAGCTGTACGAGCAGCTGTCAGGGAAG

Alignment

ORF - retro_mmus_1857 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAADISQWAGPLCLQEVDEPPQHALRVDYAGVTVDELGKVLTPTQVMNRPSSISWDGLDPGKLYTLVLTD
          MAADISQWAGPLCLQEVDEPPQHALRVDYAGVTVDELGKVLTPTQVMNRPSSISWDGLDPGKLYTLVLTD
Retrocopy MAADISQWAGPLCLQEVDEPPQHALRVDYAGVTVDELGKVLTPTQVMNRPSSISWDGLDPGKLYTLVLTD

Parental  PDAPSRKDPKFREWHHFLVVNMKGNDISSGTVLSDYVGSGPPSGTGLHRYVWLVYEQEQPLSCDEPILSN
          PDAPSRKDPKFREW.HFLVVNMKGNDISSGTVLSDYVGSGPPSGTGLHRYVWLVYEQEQPLSCDEPILSN
Retrocopy PDAPSRKDPKFREW-HFLVVNMKGNDISSGTVLSDYVGSGPPSGTGLHRYVWLVYEQEQPLSCDEPILSN

Parental  KSGDNRGKFKVETFRKKYNLGAPVAGTCYQAEWDDYVPKLYEQLSGK
          KSGDNRGKFKVETFRKKYNLGAP.AGTCYQAEWDDYVPKLYEQLSGK
Retrocopy KSGDNRGKFKVETFRKKYNLGAPAAGTCYQAEWDDYVPKLYEQLSGK

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	66.21 RPM
SRP007412_cerebellum	0.13 RPM	54.32 RPM
SRP007412_heart	0.19 RPM	46.63 RPM
SRP007412_kidney	0.29 RPM	53.36 RPM
SRP007412_liver	0.11 RPM	45.36 RPM
SRP007412_testis	0.73 RPM	301.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1857 was not detected

EST

No EST(s) were mapped for retro_mmus_1857 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_62783	249 libraries	496 libraries	321 libraries	2 libraries	4 libraries

The graphical summary, for retro_mmus_1857 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_1857 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1857 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016143	2 retrocopies	retro_amel_1355, retro_amel_754,
Bos taurus	ENSBTAG00000018115	2 retrocopies	retro_btau_1183, retro_btau_705,
Canis familiaris	ENSCAFG00000009910	1 retrocopy	retro_cfam_526,
Callithrix jacchus	ENSCJAG00000009314	2 retrocopies	retro_cjac_1410, retro_cjac_818,
Erinaceus europaeus	ENSEEUG00000003689	1 retrocopy	retro_eeur_292,
Felis catus	ENSFCAG00000002277	3 retrocopies	retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Homo sapiens	ENSG00000089220	3 retrocopies	retro_hsap_1456, retro_hsap_2288, retro_hsap_492,
Gorilla gorilla	ENSGGOG00000013281	3 retrocopies	retro_ggor_1121, retro_ggor_1701, retro_ggor_461,
Myotis lucifugus	ENSMLUG00000002259	7 retrocopies	retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta	ENSMMUG00000005098	4 retrocopies	retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furo	ENSMPUG00000002861	3 retrocopies	retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus	ENSMUSG00000032959	4 retrocopies	retro_mmus_138, retro_mmus_1857 , retro_mmus_2314, retro_mmus_542,
Nomascus leucogenys	ENSNLEG00000000322	1 retrocopy	retro_nleu_1966,
Oryctolagus cuniculus	ENSOCUG00000008395	2 retrocopies	retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii	ENSOGAG00000001740	1 retrocopy	retro_ogar_2750,
Pongo abelii	ENSPPYG00000005011	2 retrocopies	retro_pabe_1202, retro_pabe_241,
Pan troglodytes	ENSPTRG00000005512	3 retrocopies	retro_ptro_1621, retro_ptro_371, retro_ptro_992,
Rattus norvegicus	ENSRNOG00000001136	3 retrocopies	retro_rnor_1223, retro_rnor_46, retro_rnor_541,
Ictidomys tridecemlineatus	ENSSTOG00000004085	2 retrocopies	retro_itri_1603, retro_itri_961,
Tupaia belangeri	ENSTBEG00000000177	2 retrocopies	retro_tbel_272, retro_tbel_2728,
Tursiops truncatus	ENSTTRG00000000658	1 retrocopy	retro_ttru_1164,