RetrogeneDB ID: retro_mmus_3529

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:142210573..142211822(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082675
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rbbp7
• Ensembl ID: ENSMUSG00000031353
• Aliases: Rbbp7, AA409861, AI173248, AU019541, BB114024, mRbAp46
• Description: retinoblastoma binding protein 7 [Source:MGI Symbol;Acc:MGI:1194910]

Sequence

>retro_mmus_3529
ACTGTGGAGGAGCATGTCATCAACGAGGAATATAAAATCTGGAAGAAGAATACAGCGTTTCTGTAGGGCCTGGTTATGAC
CCATGCTCTTCAGTGGCCCAGTCTTACCGTTCAGTGGCTTCCTGAAGTAACTAAACCAGAAGGAAAGGATTGTGCCCTTC
ATTGGCTAATGCTGGCCACTCAAACATCTGATGAGCAGAACCATCTGGTGGTTGCTCGACTTCATATTCCCAACGATGAT
GCACAGTTTGATGCTTCCCATTGTGACAGTGACAAGGGAGAATTCGGTGGCCTTGGTTCTGTAACAAGAGAAAATTGAAT
GTGAAATTAAAATTAATCATGAAGGAGAAGTAATTCATGCTCTTTATATGCCACAGAATCCTCACATCATGGCCACAAAA
ACACCATCTTCTGATGTTTTGGTTTGTGACTATACAAAACACCCTGCAAAACCAGATCCAAGTGGAGAATGTAATCCTGA
TCTTAGATTAAGAGGTCACCAAAAGGAAGGCTATGGTCTTTCCTTGAAATCTAATTTGAGTGGGCATCTCCTGAGTGCAT
CTAATGACCATACTGTCTGCCTGTGGGATATAAATGTAGGACCAAAGGAAGGCAAAACTGTGGATGCTAAAGCAATCTTT
ACTGGCCACCCAGCTGTTGTAGAGGATGTGGCCTGGCATCTGCTGCATGAGTCCTTGTTTGGATCTGTTGCTGATGATCA
GAAACTTATGATATGGGACACCAGATCCAATACCACTTCTAAGCCGAGCCATTTGGTGGATGCACACACTGCTGAGGTCA
ACTGCCTCTCATTCAATCCCTACCGCGAGTTCATTCTAGCAACTGGCTCTGCAGATAAGACTGTAGCTTTATGGGACCTG
CGTAATCTGAAACTAAAACTCCACACCTTCGAATCGCATAAGGATGAAATTTTCCAGGTCCACTGGTCTCCACATAATGA
AGCTATTCTGGCTTCAAGTGGTACTGATCGCCGCTTGAATGTGTGGAATTTAAGTAAAATTGGAGAAGAACAATCAGCAG
AAGATGCGGAAGATGGGCCTCCAGAGCACCTGTTTATTCATGGAGGACACACTGCCAAGATTTCTGACTTCAGCTGGAAT
CCCAATGAACCTTGTGTCATTTGCTCTGTGTCTGAAGATGACATCATGCAGATATGGCAGATGGCTGAAAATATTTACAA
TGATGAAGAGTCAGATGTCACGGCATCGGAACTGGAGGGGCAAGGATCT

Alignment

ORF - retro_mmus_3529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.05 %
• Parental protein coverage: 97.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TVEERVINEEYKIWKKNTPFLYDLVMTHALQWPSLTVQWLPEVTKPEGKDYALHWLVLGTHTSDEQNHLV
          TVEE.VINEEYKIWKKNT.FL..LVMTHALQWPSLTVQWLPEVTKPEGKD.ALHWL.L.T.TSDEQNHLV
Retrocopy TVEEHVINEEYKIWKKNTAFL*GLVMTHALQWPSLTVQWLPEVTKPEGKDCALHWLMLATQTSDEQNHLV

Parental  VARVHIPNDDAQFDASHCDSDKGEFGGFGSVTG-KIECEIKINHEGEVNRARYMPQNPHIIATKTPSSDV
          VAR.HIPNDDAQFDASHCDSDKGEFGG.GSVT..KIECEIKINHEGEV..A.YMPQNPHI.ATKTPSSDV
Retrocopy VARLHIPNDDAQFDASHCDSDKGEFGGLGSVTR>KIECEIKINHEGEVIHALYMPQNPHIMATKTPSSDV

Parental  LVFDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKIVDA
          LV.DYTKHPAKPDPSGECNPDLRLRGHQKEGYGLS..SNLSGHLLSAS.DHTVCLWDIN.GPKEGK.VDA
Retrocopy LVCDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSLKSNLSGHLLSASNDHTVCLWDINVGPKEGKTVDA

Parental  KAIFTGHSAVVEDVAWHLLHESLFGSVADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCLSFNPYSEFIL
          KAIFTGH.AVVEDVAWHLLHESLFGSVADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCLSFNPY.EFIL
Retrocopy KAIFTGHPAVVEDVAWHLLHESLFGSVADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCLSFNPYREFIL

Parental  ATGSADKTVALWDLRNLKLKLHTFESHKDEIFQVHWSPHNETILASSGTDRRLNVWDLSKIGEEQSAEDA
          ATGSADKTVALWDLRNLKLKLHTFESHKDEIFQVHWSPHNE.ILASSGTDRRLNVW.LSKIGEEQSAEDA
Retrocopy ATGSADKTVALWDLRNLKLKLHTFESHKDEIFQVHWSPHNEAILASSGTDRRLNVWNLSKIGEEQSAEDA

Parental  EDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQIWQMAENIYNDEESDVTASELEGQGS
          EDGPPE.LFIHGGHTAKISDFSWNPNEP.VICSVSED.IMQIWQMAENIYNDEESDVTASELEGQGS
Retrocopy EDGPPEHLFIHGGHTAKISDFSWNPNEPCVICSVSEDDIMQIWQMAENIYNDEESDVTASELEGQGS

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	0.12 RPM	97.49 RPM
SRP007412_cerebellum	0.09 RPM	68.78 RPM
SRP007412_heart	0.09 RPM	101.80 RPM
SRP007412_kidney	0.15 RPM	93.96 RPM
SRP007412_liver	0.08 RPM	48.17 RPM
SRP007412_testis	0.18 RPM	48.12 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3529 was not detected

EST

No EST(s) were mapped for retro_mmus_3529 retrocopy.

TSS

No TSS is located nearby retro_mmus_3529 retrocopy 5' end.

Lab

retro_mmus_3529 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3529 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002820	1 retrocopy	retro_btau_1579,
Mus musculus	ENSMUSG00000031353	1 retrocopy	retro_mmus_3529 ,
Mus musculus	ENSMUSG00000040782	1 retrocopy	retro_mmus_3678,
Mus musculus	ENSMUSG00000057236	1 retrocopy	retro_mmus_356,
Oryctolagus cuniculus	ENSOCUG00000000683	1 retrocopy	retro_ocun_1939,
Otolemur garnettii	ENSOGAG00000014995	1 retrocopy	retro_ogar_2220,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Pan troglodytes	ENSPTRG00000021702	5 retrocopies	retro_ptro_1802, retro_ptro_1909, retro_ptro_2226, retro_ptro_2987, retro_ptro_896,
Rattus norvegicus	ENSRNOG00000005157	1 retrocopy	retro_rnor_1182,
Sorex araneus	ENSSARG00000008079	3 retrocopies	retro_sara_308, retro_sara_571, retro_sara_602,
Tupaia belangeri	ENSTBEG00000010151	2 retrocopies	retro_tbel_3031, retro_tbel_4341,
Tarsius syrichta	ENSTSYG00000002385	4 retrocopies	retro_tsyr_1608, retro_tsyr_1838, retro_tsyr_1957, retro_tsyr_427,