RetrogeneDB ID: retro_mmus_3602

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:40927325..40928111(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084287
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zfp259
• Ensembl ID: ENSMUSG00000032078
• Aliases: Zfp259, AI303781, ZPR1, Znf259
• Description: zinc finger protein 259 [Source:MGI Symbol;Acc:MGI:1330262]

Sequence

>retro_mmus_3602
AAGTTGTGGCATCTTAGAGAAATAACCATGAGCTTCTTTTCCTGTTAGGACTGTGGCTGGAACAACACTGAGATTCAGGC
AGCAGGCAGGATCTGGGACCAGAAGTGTACTATACCTTGACTGTTAGAGGCCAAGAGGGCATGAATGGAGACGTGGCAAA
GACAGACTTGCCACCACAAGGACACCTGGGCTGAATTTTGAAATTCCAGCTTTCAGCAAGAAGGGTGCTCTGACTACAAT
TGAGTGACTGATTAGTCACACAATCTCTGGCCTGGAACAGGACCAACCCACATGATTGTCAATGGAAGGTTTCATAGCTG
AAAGAATTGATGAATTCATTGACAAACTGAAGGACCTAAATCAAAGAGCTTCCCTTTTCACTGTGATCATTGATAATCTC
TTTGGAAACAGCTTTGTAGAAGACCCACATGCTCCCCACAAAAAAAAATTGCTTTGGTGATGACATACTATAACCAGACC
CCACAGCAAGTTGAGATACTGAGACTCCAAGCAGAAGCACAAGAAGAGAAGTAGGAAGAGGAAGACCTTAGAAATAAAGT
CTTCCAGTTCAACACAAACTTCTCAGAGTGCAATGGCATAGCTCAGACCAACAGGAAGCTTGTCCAAATCATCCTCTTTA
AAGAGGTTATCATCATGGCCACTAACTACAAGAATTGTGGACATTGAACTAATGAGATGAAGTTTAGAGAAGCAGTAGAG
CTCTTGAGTATCAGCATCACCATCCACATCACAGATCCCTCAGACATGAGCTCTTCAAGTCTGAGA

Alignment

ORF - retro_mmus_3602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.92 %
• Parental protein coverage: 60.93 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KIPFFREIIVSSFSCEHCGWNNTEIQSAGRIQDQG-VRYTLTVRSQEDMNREVVKTDS-ATTRIPELDFE
          K....REI..S.FSC..CGWNNTEIQ.AGRI.DQ..V.YTLTVR.QE.MN..V.KTD..ATTR.P.L.FE
Retrocopy KLWHLREITMSFFSC*DCGWNNTEIQAAGRIWDQK<VYYTLTVRGQEGMNGDVAKTDL<ATTRTPGLNFE

Parental  IPAFSQKGALTTVEGLISRAISGLEQDQPTRRAVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNS
          IPAFS.KGALTT.E.LIS..ISGLEQDQPT....EG.IAERIDEFI.KLKDL.Q.AS.FT..ID...GNS
Retrocopy IPAFSKKGALTTIE*LISHTISGLEQDQPT*LSMEGFIAERIDEFIDKLKDLNQRASLFTVIIDNLFGNS

Parental  FVENPHAPQKDNAL-VITYY-DRTPQQAEMLGLQAEAPEEKAEEEDLRNEVLQFNTNCPECNAPAQTNMK
          FVE.PHAP.....L.....Y...TPQQ.E.L.LQAEA.EEK.EEEDLRN.V.QFNTN..ECN..AQTN.K
Retrocopy FVEDPHAPHXXXLL<LVMTYYNQTPQQVEILRLQAEAQEEK*EEEDLRNKVFQFNTNFSECNGIAQTNRK

Parental  LVQIPHFKEVIIMATNCENCGHRTNEVKSGGAVEPLGTRITLHITDPSDMTRDLLK
          LVQI..FKEVIIMATN..NCGH.TNE.K...AVE.L...IT.HITDPSDM....L.
Retrocopy LVQIILFKEVIIMATNYKNCGH*TNEMKFREAVELLSISITIHITDPSDMSSSSLR

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	30.00 RPM
SRP007412_cerebellum	0.00 RPM	28.70 RPM
SRP007412_heart	0.06 RPM	18.15 RPM
SRP007412_kidney	0.00 RPM	26.91 RPM
SRP007412_liver	0.00 RPM	69.94 RPM
SRP007412_testis	0.00 RPM	71.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3602 was not detected

EST

No EST(s) were mapped for retro_mmus_3602 retrocopy.

TSS

No TSS is located nearby retro_mmus_3602 retrocopy 5' end.

Lab

retro_mmus_3602 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3602 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011907	1 retrocopy	retro_etel_246,
Homo sapiens	ENSG00000109917	1 retrocopy	retro_hsap_3639,
Gorilla gorilla	ENSGGOG00000000664	1 retrocopy	retro_ggor_2455,
Myotis lucifugus	ENSMLUG00000014012	1 retrocopy	retro_mluc_2167,
Macaca mulatta	ENSMMUG00000020287	1 retrocopy	retro_mmul_1808,
Mus musculus	ENSMUSG00000032078	2 retrocopies	retro_mmus_3602 , retro_mmus_3701,
Otolemur garnettii	ENSOGAG00000009977	1 retrocopy	retro_ogar_506,
Pongo abelii	ENSPPYG00000025914	1 retrocopy	retro_pabe_2986,
Pan troglodytes	ENSPTRG00000004312	1 retrocopy	retro_ptro_2464,
Sus scrofa	ENSSSCG00000015066	1 retrocopy	retro_sscr_1150,