RetrogeneDB ID: retro_mmus_2452

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:39895183..39896162(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084220
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pbk
• Ensembl ID: ENSMUSG00000022033
• Aliases: Pbk, 2810434B10Rik, AW538537, D14Ertd732e, TOPK
• Description: PDZ binding kinase [Source:MGI Symbol;Acc:MGI:1289156]

Sequence

>retro_mmus_2452
ATGGAAGGAATTAATAATTTCAAGACGCCAAACAAATTATCTGAAAAAAGGAAATCTGTATTATGTTCGACTCCATGTGT
AAATATCCCTGCCTCTCCATTTATGCAGAAGCTTGGCTTTGAGACTGGGGTCAGTGTTTACCTAATGAAAAGATCTCCAA
GAGGGTTGTCTCATTCTCCTTGGGCCATGAAAAAGATATGTCCTTTATGCGATGATCATTATCGAACTGTGTATCAGAAG
AGAGTAACTGATGAAGCTAAGATTTAAAAAAAACCTTAATCACCCAAACATTATAGGGTATCATGCTTTTACTGAAGCCA
GTGATGGTAGTCTGTGCCTTGCTATGGAATATGGAGGTGAAAAGTCTCTGAATGACTTAATAGAAGAGCAGAACAAAGAC
AGTGGAAGTCCTTTTCTAGCAGCTGTAATTCTCAGAGTTGCTTTATACATGGCCAGACGCCTAAAGTATCTGCATCAAGA
AAAGAAGCTGCTTCATGTAGACATAAAGTCTTCAAATGTTGTGATTAAAGGTGATTTTGAAACAATTAAAATCTGTGATG
TAGGAGTCTCTCTGCCGTTGGATGAAAATATGACTGTGACTGATCCTGAGGCCTGTTGTATTGGACCTGAGCCATGGAAA
CCCAAGGAACCGTTGGAAGAAAATGGCATCATTACTGACAAGGCAGATATGTTTGGTTTTGGCCTTACTCTGTGGGAAAT
GATGACTTTATGTATTCCACACATCAATCTTCCAGATGATGATGTTGATGAAGATGCAACCTTTGATGAGAGTGACTTCG
ATGATGAAGCATATTATGCAGCTCTGGGGACAAGGCCATCCATCAACATGGAAGAGCTGGATGAATCCTACCAGAAGGTC
ATTGAACTTTTCTCTGTGTGTACTAATGAGGATTCTAAAGATCACTCGTCTGCTGCTCACATCATTGAAACTTTGGAACT
AGATGGCCAATGTTGTGGT

Alignment

ORF - retro_mmus_2452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.83 %
• Parental protein coverage: 98.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGINNFKTPNK-SEKRKSVLCSTPCVNIPASPFMQKLGFGTGVSVYLMKRSPRGLSHSPWAVKKISLLC
          MEGINNFKTPNK.SEKRKSVLCSTPCVNIPASPFMQKLGF.TGVSVYLMKRSPRGLSHSPWA.KKI..LC
Retrocopy MEGINNFKTPNKLSEKRKSVLCSTPCVNIPASPFMQKLGFETGVSVYLMKRSPRGLSHSPWAMKKICPLC

Parental  DDHYRTVYQKRLTDEAKILKN-LNHPNIIGYRAFTEASDGSLCLAMEYGGEKSLNDLIEERNKDSGSPFP
          DDHYRTVYQKR.TDEAKI....LNHPNIIGY.AFTEASDGSLCLAMEYGGEKSLNDLIEE.NKDSGSPF.
Retrocopy DDHYRTVYQKRVTDEAKIXXX>LNHPNIIGYHAFTEASDGSLCLAMEYGGEKSLNDLIEEQNKDSGSPFL

Parental  AAVILRVALHMARGLKYLHQEKKLLHGDIKSSNVVIKGDFETIKICDVGVSLPLDENMTVTDPEACYIGT
          AAVILRVAL.MAR.LKYLHQEKKLLH.DIKSSNVVIKGDFETIKICDVGVSLPLDENMTVTDPEAC.IG.
Retrocopy AAVILRVALYMARRLKYLHQEKKLLHVDIKSSNVVIKGDFETIKICDVGVSLPLDENMTVTDPEACCIGP

Parental  EPWKPKEALEENGIITDKADVFAFGLTLWEMMTLCIPHVNLPDDDVDEDATFDESDFDDEAYYAALGTRP
          EPWKPKE.LEENGIITDKAD.F.FGLTLWEMMTLCIPH.NLPDDDVDEDATFDESDFDDEAYYAALGTRP
Retrocopy EPWKPKEPLEENGIITDKADMFGFGLTLWEMMTLCIPHINLPDDDVDEDATFDESDFDDEAYYAALGTRP

Parental  SINMEELDDSYQKAIELFCVCTNEDPKDRPSAAHIVEALELDGQCCG
          SINMEELD.SYQK.IELF.VCTNED.KD..SAAHI.E.LELDGQCCG
Retrocopy SINMEELDESYQKVIELFSVCTNEDSKDHSSAAHIIETLELDGQCCG

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	0.47 RPM
SRP007412_cerebellum	0.00 RPM	0.09 RPM
SRP007412_heart	0.00 RPM	0.34 RPM
SRP007412_kidney	0.00 RPM	0.73 RPM
SRP007412_liver	0.00 RPM	0.16 RPM
SRP007412_testis	0.05 RPM	50.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2452 was not detected

EST

No EST(s) were mapped for retro_mmus_2452 retrocopy.

TSS

No TSS is located nearby retro_mmus_2452 retrocopy 5' end.

Lab

retro_mmus_2452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2452 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021069	1 retrocopy	retro_btau_150,
Canis familiaris	ENSCAFG00000008369	1 retrocopy	retro_cfam_1694,
Dipodomys ordii	ENSDORG00000014896	1 retrocopy	retro_dord_697,
Myotis lucifugus	ENSMLUG00000009596	1 retrocopy	retro_mluc_713,
Monodelphis domestica	ENSMODG00000015986	1 retrocopy	retro_mdom_245,
Mus musculus	ENSMUSG00000022033	1 retrocopy	retro_mmus_2452 ,
Otolemur garnettii	ENSOGAG00000009887	1 retrocopy	retro_ogar_3495,
Tupaia belangeri	ENSTBEG00000002239	1 retrocopy	retro_tbel_3290,