RetrogeneDB ID: retro_mmus_3708

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:146599753..146600982(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081718
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zzz3
• Ensembl ID: ENSMUSG00000039068
• Aliases: Zzz3, 3110065C23Rik, 6430567E01Rik, AA408566, AI481057, AW556059, R75514
• Description: zinc finger, ZZ domain containing 3 [Source:MGI Symbol;Acc:MGI:1920453]

Sequence

>retro_mmus_3708
ATGATAGATCTTTGGTTGTACAGTTATCAGAGACTGCTACAGACCATTGCTGCTCTTGAGGCTCAGTGTTCTCAAGCAGT
ACAAGACCTGGAAAGTTTAGGCAAACATGAGAGAGAAGCACTAAAAAATCCTATTGGATTTGTGGAGAAACTTCAGAAGA
AGGCTGACATAGGGCTTCCATACCCACAGAGAGTTGTTCAGTTACCTGAGATCATGTGGAACCAGTACACCAATAGCATT
GGGAACTTTGAAAGAGAATTTAAACGCCGAAAAAAAGACATACTAGGAGAGTTAAGTTAGTTTTTGATAAAGTAGGGTTG
TCTGCTAGACCAAAAAGTCCTTTAGATCCTAAGAAGGATGGAGAATCCCTTTCATACTCTATGCTGCCTTTGAGTGATGG
TCCAGAAGGCTCCCATAATCATCCTCAGATGATAAGAGGTCGTCTGTGTGATGACAGCAAACCTGAGACCTTCAACCAGC
TGTGGACTGTTGAAGAACAGAAAAAACTCGAACAGCTACTCCTGAAATACCCTCCTGAAGAAGTAGAATCTTGGCGGTGG
CAGAAGATTGCTGATGAACTGGGCAACCAGACAGCCAAACAGGTTGCCAGTCGTGTACAGAAGTATTTCATAAAGCTAAC
AAAAGCCGGCATACCAGTTCCAGGCAGAACACCTAACTTATATATATACTCCAGAAAGTCCTCAACAAGCAGGCGACAGC
ACCCCCTTAATAAGCACCTCTTTAAACCTTCCACTTTCATGACTTCACATGAGCCACCAGTGTACATGGATGAAGATGAT
GACCGGTCTTGTCTCCATAGCCACATGAGCACTGCTGCTGAGGAGGCCTCAGATGATAAAAGCATTCCTATCATATATAG
GAGTTTACCTGAATATAAAGAACTATTACAGTTTAAAAAGTTAAAAAAGCAGAAACTTCAACAAATGCAAGCGGAAAGTG
GGTTTGTGCAGCATGTAGGCTTTAAGTCTGATAACTGTGGTGTGGAACCTAACCAAGGAGTCCGGTGGCACTGCCAGGAC
TGTCCTCCAGAAATGTCTTTGGATTTCTGTGACTCTTGTTCAGACTGCCCACATGAAACAGATACTCACAAGGAAGACCA
CCAGTTAGAACCTGTTTATAAGTCAGAGACGTTCTTAGACAGAGATTACTGTGTGTCCCAGGGCACCAGGTATAGTTACA
TGGACCCCAACTACTTCCCAGGCAACAGA

Alignment

ORF - retro_mmus_3708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MIDLWLYSYQRLLQTIAVLEAQRSQAVQDLESLGKHQREALKNPIGFVEKLQKKADIGLPYPQRVVQLPE
          MIDLWLYSYQRLLQTIA.LEAQ.SQAVQDLESLGKH.REALKNPIGFVEKLQKKADIGLPYPQRVVQLPE
Retrocopy MIDLWLYSYQRLLQTIAALEAQCSQAVQDLESLGKHEREALKNPIGFVEKLQKKADIGLPYPQRVVQLPE

Parental  IMWDQYTN-SLGNFEREFKH-RKRHTRRVKLVFDKVGLPARPKSPLDPKKDGESLSYSMLPLSDGPEGSH
          IMW.QYTN..LG..........KRHTRRVKLVFDKVGL.ARPKSPLDPKKDGESLSYSMLPLSDGPEGSH
Retrocopy IMWNQYTN>ALGTLKENLNA>KKRHTRRVKLVFDKVGLSARPKSPLDPKKDGESLSYSMLPLSDGPEGSH

Parental  NRPQMIRGRLCDDSKPETFNQLWTVEEQKKLEQLLLKYPPEEVESRRWQKIADELGNRTAKQVASRVQKY
          N.PQMIRGRLCDDSKPETFNQLWTVEEQKKLEQLLLKYPPEEVES.RWQKIADELGN.TAKQVASRVQKY
Retrocopy NHPQMIRGRLCDDSKPETFNQLWTVEEQKKLEQLLLKYPPEEVESWRWQKIADELGNQTAKQVASRVQKY

Parental  FIKLTKAGIPVPGRTPNLYIYSRKSSTSRRQHPLNKHLFKPSTFMTSHEPPVYMDEDDDRSCLHSHMSTA
          FIKLTKAGIPVPGRTPNLYIYSRKSSTSRRQHPLNKHLFKPSTFMTSHEPPVYMDEDDDRSCLHSHMSTA
Retrocopy FIKLTKAGIPVPGRTPNLYIYSRKSSTSRRQHPLNKHLFKPSTFMTSHEPPVYMDEDDDRSCLHSHMSTA

Parental  AEEASDEESIPIIYRSLPEYKELLQFKKLKKQKLQQMQAESGFVQHVGFKCDNCGVEPIQGVRWHCQDCP
          AEEASD..SIPIIYRSLPEYKELLQFKKLKKQKLQQMQAESGFVQHVGFK.DNCGVEP.QGVRWHCQDCP
Retrocopy AEEASDDKSIPIIYRSLPEYKELLQFKKLKKQKLQQMQAESGFVQHVGFKSDNCGVEPNQGVRWHCQDCP

Parental  PEMSLDFCDSCSDCPHETDIHKEDHQLEPVYKSETFLDRDYCVSQGTSYSYLDPNYFPANR
          PEMSLDFCDSCSDCPHETD.HKEDHQLEPVYKSETFLDRDYCVSQGT.YSY.DPNYFP.NR
Retrocopy PEMSLDFCDSCSDCPHETDTHKEDHQLEPVYKSETFLDRDYCVSQGTRYSYMDPNYFPGNR

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	60.91 RPM
SRP007412_cerebellum	0.26 RPM	48.46 RPM
SRP007412_heart	0.06 RPM	34.93 RPM
SRP007412_kidney	0.33 RPM	57.09 RPM
SRP007412_liver	0.05 RPM	29.93 RPM
SRP007412_testis	0.27 RPM	40.25 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3708 was not detected

EST

No EST(s) were mapped for retro_mmus_3708 retrocopy.

TSS

No TSS is located nearby retro_mmus_3708 retrocopy 5' end.

Lab

retro_mmus_3708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3708 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000039068	1 retrocopy	retro_mmus_3708 ,
Oryctolagus cuniculus	ENSOCUG00000002167	1 retrocopy	retro_ocun_511,