RetrogeneDB ID: retro_mmus_3701

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:138522505..138523244(-)
• Located in intron of: ENSMUSG00000059203

Retrocopy information

• Ensembl ID: ENSMUSG00000081017
• 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_3701
AAAGCAAATGACTCAGTGATCACATACTACATCCGGATTCCACAGCAAGCTGAGATGCTGTGGCTCCAAGCAGGAGAACC
TGAGAAATCACAAGAGAATGAACTTAGAAACAAAGTGTACCATTTCAACACAAACTGCCCAGAGTGCAATGCTCCAGCTG
AAACCAACATGAACCTTGTCCAAAATCTCCCCCACTTTAAAGAGGTTATGATCATGGACACCAACTGTGAGAATTGTAGG
CATCAGAATAATGAGGTGAAGTCTGGAGAAGCAGTAGAGTCCTTGGGTACCAGAATAATTCTTTACATCACAGTTCCCTC
AGACATGACCAGAGACCTACTTAAGTCTGACACTTGTAGTGTGGAACTCTCCGAACTTGAGATTGAACTGGGAATGACTG
TCCTTAAGGTCAAGCTCATCACTCTAGAAGAATTGATGAAAAACATCTGAGAATTGATAACTAAGAACCCATTCACACTG
GGTGACAGCTCGAATCCTGACCAGTTGGAGAAACTTCAGGGGCTTAGCTAGAAGTTTAATCATATCACTGAGGGCAAGAT
GAAGGCCCACTTTTTTCATGAATGGTCCAGCAGGAAACAGTTACCTGAAGAATGTCTATGCACCTGAAGATGATCCGCAG
ATGAAGGTATAGCCATACAAGCACACCTTTGACCAAAATGAGGAGCTCAGCCCCTATGACTTGAAGACAGAAGGCTATGA
GGGAGGTCTGGCCCCACAG

Alignment

ORF - retro_mmus_3701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.79 %
• Parental protein coverage: 53.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDNALVITYYDRTPQQAEMLGLQAEAPEEKAEEEDLRNEVLQFNTNCPECNAPAQTNMKLVQ-IPHFKEV
          K.N..VITYY.R.PQQAEML.LQA..PE.K..E..LRN.V..FNTNCPECNAPA.TNM.LVQ..PHFKEV
Retrocopy KANDSVITYYIRIPQQAEMLWLQAGEPE-KSQENELRNKVYHFNTNCPECNAPAETNMNLVQNLPHFKEV

Parental  IIMATNCENCGHRTNEVKSGGAVEPLGTRITLHITDPSDMTRDLLKSETCSVEIPELEFELGMAVLGGKF
          .IM.TNCENC.H..NEVKSG.AVE.LGTRI.L.IT.PSDMTRDLLKS.TCSVE..ELE.ELGM.VL..K.
Retrocopy MIMDTNCENCRHQNNEVKSGEAVESLGTRIILYITVPSDMTRDLLKSDTCSVELSELEIELGMTVLKVKL

Parental  TTLEGLLKDIRELVTKNPFTLGDSSNPDQSEKLQEFSQKLGQIIEGKMKAH-FIMNDPAGNSYLQNVYAP
          .TLE.L.K.I.EL.TKNPFTLGDSSNPDQ.EKLQ..S.K...I.EGKMKAH.F.MN.PAGNSYL.NVYAP
Retrocopy ITLEELMKNI*ELITKNPFTLGDSSNPDQLEKLQGLS*KFNHITEGKMKAH>FFMNGPAGNSYLKNVYAP

Parental  EDDPEMKVERYKRTFDQNEELGLNDMKTEGYEAGLAPQ
          EDDP.MKV..YK.TFDQNEEL...D.KTEGYE.GLAPQ
Retrocopy EDDPQMKV*PYKHTFDQNEELSPYDLKTEGYEGGLAPQ

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	0.02 RPM	30.00 RPM
SRP007412_cerebellum	0.00 RPM	28.70 RPM
SRP007412_heart	0.00 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_3701 was not detected

EST

No EST(s) were mapped for retro_mmus_3701 retrocopy.

TSS

No TSS is located nearby retro_mmus_3701 retrocopy 5' end.

Lab

retro_mmus_3701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3701 has 0 orthologous retrocopies within eutheria group .

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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,