RetrogeneDB ID: retro_mmus_1452

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:23034077..23034526(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Wrb
• Ensembl ID: ENSMUSG00000023147
• Aliases: Wrb, 5530402J05Rik, C030018G21Rik, Chd5
• Description: tryptophan rich basic protein [Source:MGI Symbol;Acc:MGI:2136882]

Sequence

>retro_mmus_1452
CGCATCCTCCTTCTGTCCCTGACATCCTTTATTTCCAGAGTGCTGCAGAAGGATGAAGAACAGGAGTCATGGATGAGAGC
TGAGATACAGGACATGAAGCAGGAGCTGTCTGCTGTCAACATGATGGAAGAGTTTGCCAGATACACCAGGCTGGAAAGGA
AGATCAACAAAATCACAGACAAACTCAAAACTCATGTGAAGGCATGGATAGCTCAGTTGGCCAAGATCAAGTGGTTCGTG
AGTGTTGCTTTCTACATTCTGCAAGCAGCGCTGATGATCTCACTAATATGGAAGTATTACTCCGTCCCAGTATCTGTGAT
GCCCAGCAAGGGGATCACCCCACTGGACTGCCTGGTAGTCTTTCCTCTTGAGTAGCAGGTGGAATTGGAATCACCTGTTG
GATTTTAGTCTGTAACAAAGTTGTGGCTATCATTCTCCACACTTTCAGC

Alignment

ORF - retro_mmus_1452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.43 %
• Parental protein coverage: 86.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RILLPSLSSFISRVLQKDAEQESQMRAEIQGMKQELSTVNMMDEFARYARLERKINKMTDKLKTHVKART
          RILL.SL.SFISRVLQKD.EQES.MRAEIQ.MKQELS.VNMM.EFARY.RLERKINK.TDKLKTHVKA..
Retrocopy RILLLSLTSFISRVLQKDEEQESWMRAEIQDMKQELSAVNMMEEFARYTRLERKINKITDKLKTHVKAWI

Parental  AQLAKIKWFISVAFYILQAALMISLIWKYYSVPVAVVPSKWITPLDRLVAFPTR-VAGGIGITCWILVCN
          AQLAKIKWF.SVAFYILQAALMISLIWKYYSVPV.V.PSK.ITPLD.LV.FP...VAGGIGITCWILVCN
Retrocopy AQLAKIKWFVSVAFYILQAALMISLIWKYYSVPVSVMPSKGITPLDCLVVFPLE<VAGGIGITCWILVCN

Parental  KVVAIVLHPFS
          KVVAI.LH.FS
Retrocopy KVVAIILHTFS

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	53.34 RPM
SRP007412_cerebellum	0.00 RPM	62.05 RPM
SRP007412_heart	0.00 RPM	10.99 RPM
SRP007412_kidney	1.60 RPM	12.69 RPM
SRP007412_liver	0.05 RPM	4.48 RPM
SRP007412_testis	0.05 RPM	10.34 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1452 was not detected

EST

No EST(s) were mapped for retro_mmus_1452 retrocopy.

TSS

No TSS is located nearby retro_mmus_1452 retrocopy 5' end.

Lab

retro_mmus_1452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1452 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005714	2 retrocopies	retro_cjac_2153, retro_cjac_3208,
Dasypus novemcinctus	ENSDNOG00000024987	1 retrocopy	retro_dnov_1496,
Homo sapiens	ENSG00000182093	1 retrocopy	retro_hsap_3080,
Gorilla gorilla	ENSGGOG00000013144	1 retrocopy	retro_ggor_2116,
Microcebus murinus	ENSMICG00000015808	1 retrocopy	retro_mmur_1275,
Macaca mulatta	ENSMMUG00000020654	2 retrocopies	retro_mmul_1966, retro_mmul_853,
Mus musculus	ENSMUSG00000023147	1 retrocopy	retro_mmus_1452 ,
Nomascus leucogenys	ENSNLEG00000013146	1 retrocopy	retro_nleu_2014,
Otolemur garnettii	ENSOGAG00000026761	1 retrocopy	retro_ogar_2691,
Pongo abelii	ENSPPYG00000011427	1 retrocopy	retro_pabe_2552,
Pan troglodytes	ENSPTRG00000013915	1 retrocopy	retro_ptro_2078,
Ictidomys tridecemlineatus	ENSSTOG00000012736	1 retrocopy	retro_itri_1744,
Tursiops truncatus	ENSTTRG00000015373	1 retrocopy	retro_ttru_1711,