RetrogeneDB ID: retro_mmus_1487

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:11190252..11190958(-)
• Located in intron of: ENSMUSG00000096959

Retrocopy information

• Ensembl ID: ENSMUSG00000081052
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Wdr45b
• Ensembl ID: ENSMUSG00000025173
• Aliases: Wdr45b, 0610008N23Rik, AA408735, D16Bwg0193e, WIPI-3, Wdr45l
• Description: WD repeat domain 45B [Source:MGI Symbol;Acc:MGI:1914090]

Sequence

>retro_mmus_1487
AGAGATAGAATTGTGGTGGTTCTGGACTCCATGATTAAGGTGTTCACACTCACACACAATCCCTACCAGTTGCACGTCTT
TGAAACCTGCTATAATCCTAAAGGCCTCTGTGTCCTGTGTCCCAACAGTAACAACTCCCTTCTTGCCTTCCCTGACACTC
ACACTGGCCATGTACAGTTTGTGGACCTGCCAACACTGAAAAGCCACCAGAGGACATTCCCGCACATGAGGGTGTCCTGA
GCTGTATTGCTCTCAACTTACAGGGAACAAGAATTGCAACTGCATCTGAAAAAGGGACCCTTATAAGAATATTTGATACT
TCATTGGGGCATTTAATCCAGGAGCTACGAAGAGGATCTCAAGCAGCCAATATCTATTGCATCAACTTCAATCAGGATGC
TTCTCTCATCTGTGTGTCCAGTGATCACGGCACTGTGCACATTTTTGTAGCCGAAGATCCAAAAAGCAATAACAGTATAG
TTTGGCATCAGCCACTTTCCTTCCAAAATACTTCAGCTCCAAATGGAGTTTTTCCAAGTTTCAGGTTCCTTCAGGCTCGC
CATGCATCTGTGCCTTTGGAACAGAGCCCAATGCAGTCATCGCTATCTGTGCAGATGGCAGCTACTACAAGTTCCTGTTC
AGTCCTAAGGGCAAGTGTGTCCTGGACGTGTGTGCACAGTTCCTAGAGATGACCGATGACAAGCTG

Alignment

ORF - retro_mmus_1487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.28 %
• Parental protein coverage: 68.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDRIVVVLDSMIKVFTFTHNPHQLHVFETCYNPKGLCVLCPNSNNSLLAFPGTHTGHVQLVDL-ASTEKP
          RDRIVVVLDSMIKVFT.THNP.QLHVFETCYNPKGLCVLCPNSNNSLLAFP.THTGHVQ.VDL.A.TEKP
Retrocopy RDRIVVVLDSMIKVFTLTHNPYQLHVFETCYNPKGLCVLCPNSNNSLLAFPDTHTGHVQFVDL<ANTEKP

Parental  PVDIPAHEGVLSCIALNLQGTRIATASEKGTLIRIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICV
          P.DIPAHEGVLSCIALNLQGTRIATASEKGTLIRIFDTS.GHLIQELRRGSQAANIYCINFNQDASLICV
Retrocopy PEDIPAHEGVLSCIALNLQGTRIATASEKGTLIRIFDTSLGHLIQELRRGSQAANIYCINFNQDASLICV

Parental  SSDHGTVHIFAAEDPKRNK-QSSLASASFLPKYFSSKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGS
          SSDHGTVHIF.AEDPK.N..Q.SLASA.FLPKYFSSKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGS
Retrocopy SSDHGTVHIFVAEDPKSNN<QYSLASATFLPKYFSSKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGS

Parental  YYKFLFSPKGECVRDVCAQFLEMTDDKL
          YYKFLFSPKG.CV.DVCAQFLEMTDDKL
Retrocopy YYKFLFSPKGKCVLDVCAQFLEMTDDKL

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	0.09 RPM	46.91 RPM
SRP007412_cerebellum	0.00 RPM	32.31 RPM
SRP007412_heart	0.03 RPM	27.55 RPM
SRP007412_kidney	0.08 RPM	29.74 RPM
SRP007412_liver	0.11 RPM	35.53 RPM
SRP007412_testis	2.97 RPM	16.15 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1487 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	16:11190883..11191412
ENCFF001YKA	POLR2A	16:11191786..11198940
ENCFF001YKA	POLR2A	16:11190398..11191464

EST

No EST(s) were mapped for retro_mmus_1487 retrocopy.

TSS

No TSS is located nearby retro_mmus_1487 retrocopy 5' end.

Lab

retro_mmus_1487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1487 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005657	1 retrocopy	retro_cpor_322,
Homo sapiens	ENSG00000141580	2 retrocopies	retro_hsap_1820, retro_hsap_1879,
Gorilla gorilla	ENSGGOG00000006132	2 retrocopies	retro_ggor_1376, retro_ggor_2173,
Macropus eugenii	ENSMEUG00000013344	1 retrocopy	retro_meug_233,
Macaca mulatta	ENSMMUG00000021803	1 retrocopy	retro_mmul_1330,
Mus musculus	ENSMUSG00000025173	1 retrocopy	retro_mmus_1487 ,
Nomascus leucogenys	ENSNLEG00000010516	1 retrocopy	retro_nleu_1227,
Pongo abelii	ENSPPYG00000008785	2 retrocopies	retro_pabe_150, retro_pabe_1559,
Pan troglodytes	ENSPTRG00000009807	3 retrocopies	retro_ptro_1171, retro_ptro_1262, retro_ptro_2912,
Pteropus vampyrus	ENSPVAG00000006212	1 retrocopy	retro_pvam_158,