RetrogeneDB ID: retro_mmus_1388

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:36120000..36120504(-)
• Located in intron of: ENSMUSG00000037627

Retrocopy information

• Ensembl ID: ENSMUSG00000092230
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hnrnpc
• Ensembl ID: ENSMUSG00000060373
• Aliases: Hnrnpc, AL022939, D14Wsu171e, Hnrpc, Hnrpc1, Hnrpc2, hnRNPC1, hnRNPC2, hnrnp-C
• Description: heterogeneous nuclear ribonucleoprotein C [Source:MGI Symbol;Acc:MGI:107795]

Sequence

>retro_mmus_1388
ATTGCTTGAGCTGTGGTGCCTTCCACACTGCAGTGTGTTTTGGGGAACACCTCATGAAGGGGCAAAAGTAGATTCAATTC
GAAGAGTGGACCATGGGGATCTTCTTCCAAGTCTGGAAAGTTGAAAGGTGATGACCTTCAGGCCATTAAAAAGGAGCTGA
CTCAGATAAAACAAAAAGTGGATTCTCTTCTGGAAAGCCTGGAAAAAACTGAAAAAGAACAAAGCAAGCAAGCAGGCTTG
TCCTTCTCGTCCCCGGTAGAGATGAAGAGTGAAAAGTTTGAAGAAGAGCAGAGCAGCGCCTCTGTGAAGAAAGACGGCAC
TGATGGGAAGATGGAGTCGGAGGCAGGTGCAGGTGACTCTGCTGAGGAGGGTGACCTACTGGATGATGACGATGATGAAG
ATTAGGGGCAGGGGGAGGAGCATGACCAGCTGGAGGTGAAGGATGATGAAAAAGAGCCTGAGGAAGGAGATGACAGAGAC
AGCGACAGTGGGGAGGACGACTCT

Alignment

ORF - retro_mmus_1388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.43 %
• Parental protein coverage: 52.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IARAVVPSKRQRVSGNTSRRGKSGFNSKSGQRGSSSKSGKLKGDDLQAIKKELTQIKQKVDSLLESLEKI
          IA.AVVPS..Q.V.GNTS.RGKS.FNSKSG..GSSSKSGKLKGDDLQAIKKELTQIKQKVDSLLESLEK.
Retrocopy IA*AVVPSTLQCVLGNTS*RGKSRFNSKSGPWGSSSKSGKLKGDDLQAIKKELTQIKQKVDSLLESLEKT

Parental  EKEQSKQADLSFSSPVEMKNEKSEEEQSSASVKKDETNVKMESEAGADDSAEEGDLLDDDDNEDRGD---
          EKEQSKQA.LSFSSPVEMK.EK.EEEQSSASVKKD.T..KMESEAGA.DSAEEGDLLDDDD.ED.G....
Retrocopy EKEQSKQAGLSFSSPVEMKSEKFEEEQSSASVKKDGTDGKMESEAGAGDSAEEGDLLDDDDDED*GQGEE

Parental  -DQLELKDDEKEPEEGEDDRDSANGEDDS
          .DQLE.KDDEKEPEEG.DDRDS..GEDDS
Retrocopy HDQLEVKDDEKEPEEG-DDRDSDSGEDDS

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	0.00 RPM	110.48 RPM
SRP007412_cerebellum	0.00 RPM	121.32 RPM
SRP007412_heart	0.00 RPM	68.55 RPM
SRP007412_kidney	0.04 RPM	87.30 RPM
SRP007412_liver	0.00 RPM	63.96 RPM
SRP007412_testis	0.41 RPM	61.02 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1388 was not detected

EST

No EST(s) were mapped for retro_mmus_1388 retrocopy.

TSS

No TSS is located nearby retro_mmus_1388 retrocopy 5' end.

Lab

retro_mmus_1388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1388 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005504	1 retrocopy	retro_cfam_1140,
Homo sapiens	ENSG00000092199	2 retrocopies	retro_hsap_1624, retro_hsap_3740,
Gorilla gorilla	ENSGGOG00000023015	1 retrocopy	retro_ggor_1046,
Macaca mulatta	ENSMMUG00000014809	4 retrocopies	retro_mmul_1112, retro_mmul_205, retro_mmul_468, retro_mmul_503,
Mustela putorius furo	ENSMPUG00000000164	2 retrocopies	retro_mputfur_231, retro_mputfur_241,
Mus musculus	ENSMUSG00000060373	1 retrocopy	retro_mmus_1388 ,
Nomascus leucogenys	ENSNLEG00000014362	2 retrocopies	retro_nleu_1828, retro_nleu_59,
Oryctolagus cuniculus	ENSOCUG00000015029	1 retrocopy	retro_ocun_138,
Otolemur garnettii	ENSOGAG00000012543	1 retrocopy	retro_ogar_165,
Pongo abelii	ENSPPYG00000005593	6 retrocopies	retro_pabe_1116, retro_pabe_1263, retro_pabe_1342, retro_pabe_2, retro_pabe_722, retro_pabe_780,
Pan troglodytes	ENSPTRG00000006118	2 retrocopies	retro_ptro_1089, retro_ptro_2539,
Rattus norvegicus	ENSRNOG00000011621	1 retrocopy	retro_rnor_922,
Tupaia belangeri	ENSTBEG00000011514	11 retrocopies	retro_tbel_1738, retro_tbel_2114, retro_tbel_2475, retro_tbel_2838, retro_tbel_2849, retro_tbel_3094, retro_tbel_3293, retro_tbel_3776, retro_tbel_3903, retro_tbel_3937, retro_tbel_818,
Tarsius syrichta	ENSTSYG00000003305	3 retrocopies	retro_tsyr_1004, retro_tsyr_1326, retro_tsyr_1411,
Tursiops truncatus	ENSTTRG00000016055	2 retrocopies	retro_ttru_1299, retro_ttru_1490,