RetrogeneDB ID: retro_mmus_1750

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:9335194..9335413(-)
• Located in intron of: ENSMUSG00000024286

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Hspe1
• Ensembl ID: ENSMUSG00000073676
• Aliases: Hspe1, 10kDa, Hsp10, mt-cpn10
• Description: heat shock protein 1 (chaperonin 10) [Source:MGI Symbol;Acc:MGI:104680]

Sequence

>retro_mmus_1750
GGTGCCATTATGCTTCCGGAAAAGTCGCAAGGAAAAGTATTTCAAGCAATGGTTGTGGCTGTGGGGTCGGGCGGGAAAGG
AAAGGGTGGAGAGATTCAGCCTGTAAGCGTGAAAGTTAGAGAGAAACTTCTCCCAGAATATAGAGGCACCAAAGTAGTTC
TAGACGACAAGGATTATGCCTTATTTAGAGATAGTGACATTCTTGGAAAATATGTTGAC

Alignment

ORF - retro_mmus_1750 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 72.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGIMLPEKSQGKVLQATVVAVGSGGKGKSGEIEPVSVKVGDKVLLPEYGGTKVVLDDKDYFLFRDSDILG
          G.IMLPEKSQGKV.QA.VVAVGSGGKGK.GEI.PVSVKV..K.LLPEY.GTKVVLDDKDY.LFRDSDILG
Retrocopy GAIMLPEKSQGKVFQAMVVAVGSGGKGKGGEIQPVSVKVREK-LLPEYRGTKVVLDDKDYALFRDSDILG

Parental  KYVD
          KYVD
Retrocopy KYVD

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	19.06 RPM
SRP007412_cerebellum	0.09 RPM	18.80 RPM
SRP007412_heart	0.03 RPM	39.32 RPM
SRP007412_kidney	0.06 RPM	64.04 RPM
SRP007412_liver	0.03 RPM	64.07 RPM
SRP007412_testis	0.00 RPM	5.95 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1750 was not detected

EST

No EST(s) were mapped for retro_mmus_1750 retrocopy.

TSS

No TSS is located nearby retro_mmus_1750 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: TAGTGTTGTGACATGTGTTCT (21 nt long)
• Reverse primer: GACACCATTTCAACAGTGATT (21 nt long)
• Annealing temperature: 50 °C
• (Expected) product size: 398
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1750 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 111 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013769	18 retrocopies	retro_amel_1027, retro_amel_1083, retro_amel_1084, retro_amel_1100, retro_amel_133, retro_amel_1504, retro_amel_1513, retro_amel_1623, retro_amel_1699, retro_amel_1819, retro_amel_199, retro_amel_23, retro_amel_269, retro_amel_310, retro_amel_329, retro_amel_491, retro_amel_506, retro_amel_922,
Canis familiaris	ENSCAFG00000010890	4 retrocopies	retro_cfam_1768, retro_cfam_1883, retro_cfam_208, retro_cfam_556,
Choloepus hoffmanni	ENSCHOG00000007417	17 retrocopies	retro_chof_1048, retro_chof_1160, retro_chof_143, retro_chof_1476, retro_chof_1561, retro_chof_1755, retro_chof_1880, retro_chof_2052, retro_chof_2053, retro_chof_226, retro_chof_303, retro_chof_414, retro_chof_420, retro_chof_86, retro_chof_907, retro_chof_91, retro_chof_940,
Callithrix jacchus	ENSCJAG00000004008	1 retrocopy	retro_cjac_254,
Felis catus	ENSFCAG00000014455	9 retrocopies	retro_fcat_114, retro_fcat_1174, retro_fcat_1406, retro_fcat_1686, retro_fcat_1723, retro_fcat_457, retro_fcat_681, retro_fcat_794, retro_fcat_97,
Gorilla gorilla	ENSGGOG00000027944	17 retrocopies	retro_ggor_1051, retro_ggor_117, retro_ggor_1243, retro_ggor_1545, retro_ggor_157, retro_ggor_1676, retro_ggor_1821, retro_ggor_1956, retro_ggor_1957, retro_ggor_1958, retro_ggor_2331, retro_ggor_2391, retro_ggor_2476, retro_ggor_2492, retro_ggor_775, retro_ggor_841, retro_ggor_897,
Loxodonta africana	ENSLAFG00000000057	1 retrocopy	retro_lafr_69,
Macaca mulatta	ENSMMUG00000010491	1 retrocopy	retro_mmul_344,
Mus musculus	ENSMUSG00000073676	11 retrocopies	retro_mmus_1005, retro_mmus_1719, retro_mmus_1750 , retro_mmus_1934, retro_mmus_2483, retro_mmus_2485, retro_mmus_301, retro_mmus_3077, retro_mmus_386, retro_mmus_872, retro_mmus_877,
Oryctolagus cuniculus	ENSOCUG00000010360	1 retrocopy	retro_ocun_127,
Otolemur garnettii	ENSOGAG00000034434	24 retrocopies	retro_ogar_1018, retro_ogar_1441, retro_ogar_1512, retro_ogar_1690, retro_ogar_1744, retro_ogar_1899, retro_ogar_191, retro_ogar_1921, retro_ogar_200, retro_ogar_2030, retro_ogar_2129, retro_ogar_2310, retro_ogar_235, retro_ogar_2439, retro_ogar_2636, retro_ogar_2928, retro_ogar_3088, retro_ogar_3350, retro_ogar_3419, retro_ogar_389, retro_ogar_777, retro_ogar_824, retro_ogar_829, retro_ogar_834,
Pongo abelii	ENSPPYG00000025876	1 retrocopy	retro_pabe_179,
Rattus norvegicus	ENSRNOG00000014868	6 retrocopies	retro_rnor_1094, retro_rnor_1320, retro_rnor_1334, retro_rnor_2245, retro_rnor_2296, retro_rnor_984,