RetrogeneDB ID: retro_mmus_3584

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:20842214..20842474(-)
• Located in intron of: ENSMUSG00000001127

Retrocopy information

• Ensembl ID: ENSMUSG00000082393
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hrsp12
• Ensembl ID: ENSMUSG00000022323
• Aliases: Hrsp12, HR12, HRP12
• Description: heat-responsive protein 12 [Source:MGI Symbol;Acc:MGI:1095401]

Sequence

>retro_mmus_3584
ATCTCATCCCTAATCAGAAAGGTGATCAGCACCACAAAAGCCCCGGTGGTCATTGGTGCCTACAGCCAAGCTGTGCTAGT
GGACAGACCATTTGCATGTCTAGACAGGTAGGCATGGATCCTTCCAGTGGACAGCTTGTTCCAAGAGGGGTAATAAAAGA
AGCTAAGCGGGCCTTTAAAAACGTGGGTGAGATTCTTAAAGCTGCAGGTTGTGATTTCACTAATGTGGTGAAAACAACTG
TTTTACTGGCTGACATAAAC

Alignment

ORF - retro_mmus_3584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.41 %
• Parental protein coverage: 64.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSIIRKVISTTKAPAAIGPYSQAVQVDR-TIYISGQVGLDPSSGQLVPGGVVEEAKQALKNLGEILKAA
          .SS.IRKVISTTKAP..IG.YSQAV.VDR.TI..S.QVG.DPSSGQLVP.GV..EAK.A.KN.GEILKAA
Retrocopy ISSLIRKVISTTKAPVVIGAYSQAVLVDR<TICMSRQVGMDPSSGQLVPRGVIKEAKRAFKNVGEILKAA

Parental  GCDFNNVVKTTVLLADMN
          GCDF.NVVKTTVLLAD.N
Retrocopy GCDFTNVVKTTVLLADIN

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	21.24 RPM
SRP007412_cerebellum	0.04 RPM	42.21 RPM
SRP007412_heart	0.00 RPM	5.76 RPM
SRP007412_kidney	0.02 RPM	526.27 RPM
SRP007412_liver	0.03 RPM	522.66 RPM
SRP007412_testis	0.00 RPM	1.14 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3584 was not detected

EST

No EST(s) were mapped for retro_mmus_3584 retrocopy.

TSS

No TSS is located nearby retro_mmus_3584 retrocopy 5' end.

Lab

retro_mmus_3584 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3584 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030250	1 retrocopy	retro_cfam_668,
Choloepus hoffmanni	ENSCHOG00000001278	8 retrocopies	retro_chof_133, retro_chof_1972, retro_chof_2434, retro_chof_2503, retro_chof_2676, retro_chof_380, retro_chof_515, retro_chof_757,
Callithrix jacchus	ENSCJAG00000015560	2 retrocopies	retro_cjac_1702, retro_cjac_465,
Dasypus novemcinctus	ENSDNOG00000025138	3 retrocopies	retro_dnov_1155, retro_dnov_224, retro_dnov_793,
Erinaceus europaeus	ENSEEUG00000014805	1 retrocopy	retro_eeur_256,
Gorilla gorilla	ENSGGOG00000001185	1 retrocopy	retro_ggor_1153,
Loxodonta africana	ENSLAFG00000002078	1 retrocopy	retro_lafr_437,
Macaca mulatta	ENSMMUG00000011825	2 retrocopies	retro_mmul_558, retro_mmul_88,
Monodelphis domestica	ENSMODG00000006575	1 retrocopy	retro_mdom_319,
Mus musculus	ENSMUSG00000022323	1 retrocopy	retro_mmus_3584 ,
Ornithorhynchus anatinus	ENSOANG00000021532	1 retrocopy	retro_oana_33,
Otolemur garnettii	ENSOGAG00000001465	3 retrocopies	retro_ogar_2308, retro_ogar_2951, retro_ogar_552,
Ictidomys tridecemlineatus	ENSSTOG00000011452	4 retrocopies	retro_itri_1591, retro_itri_192, retro_itri_605, retro_itri_894,
Tupaia belangeri	ENSTBEG00000002602	10 retrocopies	retro_tbel_1543, retro_tbel_1602, retro_tbel_2450, retro_tbel_2868, retro_tbel_2995, retro_tbel_3589, retro_tbel_421, retro_tbel_621, retro_tbel_888, retro_tbel_953,