RetrogeneDB ID: retro_mmus_1078

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:14220991..14221938(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Zscan5b
• Ensembl ID: ENSMUSG00000058028
• Aliases: Zscan5b, Zfg1, Zfp371
• Description: zinc finger and SCAN domain containing 5B [Source:MGI Symbol;Acc:MGI:2159640]

Sequence

>retro_mmus_1078
ATGGCTATGAATGTGCCATCAGAGAGCCTTGTCAAATCGGGGCAGCCCCTATCACTAATATCCCAGGTAAAACATGGAGA
AAGGCAAAACTACAACTCCCATCTTTGACACATGAAGTTCCGAGGTTTCAGTCTCATGGAAGTGTCCAACATGATCCAGG
ATCTCAGGAGAATCTCTGAGCTATGAGAATCTCTGAGGCCAGACCTGAACAGCAAGGAGGAGATTCTGGATCAAGTGGTG
TTGGAGCAGTTCGTATCTACATGCCACCAGAGCTGCAGGCCTTAGTGAAGGAGCGCAAAGTGAAGAGCTGCAAAGACCTG
GAAAAGATGCTGAGGGACGGGAAACGCCACACTGATCCATAATTTCCTCCCAAGGACAGGCATACACCTCCTTCCCAGCG
TTGGGAAGGCTGAAGCCACAGAGTTTGATAAACGGGATCATATGTGGATTTGTCCCACAAATTTGAGCACTTATCAAATG
AGAGCGAGGGGTCTCTCAACAGAGGCCAGGCCAGCCGAGAGCTGCAGAACCTCTGAGACTGAAGAGCCATCCACCAGCCA
GGTGAGTGGAGAGGACGTTTTGCTGGGAGTAATTCCTGAGAGGAGACAGCCAGACTACCTGAGACCTGAGTAGGGCCTGG
GGAATGACTCAGTCCCTGATTGGGAAGAGGGGGAGGCATCTGTGTTTGTTGGTCAGGACCCTCATCCAACACTGTGTCCT
GCTGGTTCCCTCAGAGTAAAACATGTCGTGCTGCCCCAAGAAGACACTTTTTGGATGCTGTGCTATCGTTCACCCATATT
CTGGAAGAGATTTAGTCTTGAACAGGGATCTTCAGAGTATTTGTTCGTGCTTTCAACTTACCCACTTCCCAAAGAGTGGC
GTCCTATATGGGCAATACAGAAGATGGGCTAGAGGCTGCTAATCCAGAGCCTGCTAGCCCACGGCCT

Alignment

ORF - retro_mmus_1078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 66.88 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MATNVPPDSPVRSGQSVSLISQVKHGERQNYNPEFWHVKFRGFSPSEGSNWIQDLRSISELCYQWLRPDL
          MA.NVP..S.V.SGQ..SLISQVKHGERQNYN....H.KFRGFS..E.SN.IQDLR.ISEL....LRPDL
Retrocopy MAMNVPSESLVKSGQPLSLISQVKHGERQNYNSHL*HMKFRGFSLMEVSNMIQDLRRISEL-*ESLRPDL

Parental  NSKEEILDQLVLEQFL-ICMPPEQQALVKESGVKSCKDLEKLLRDRKRH-NWSIIYSQGQAHLLRHPSVG
          NSKEEILDQ.VLEQF..I.MPPE.QALVKE..VKSCKDLEK.LRD.KRH...SII.SQGQA.....P..G
Retrocopy NSKEEILDQVVLEQFV<IYMPPELQALVKERKVKSCKDLEKMLRDGKRH<H*SIISSQGQAY-TSFPALG

Parental  -KAEAAE-DKWGHTDFSQEHLSNESEESLNRGQASRELQN--LSETEEPSTSQEEG--ILLGVIPERRQP
          .KAEA.E.DK..H.......LS.............R.......SETEEPSTSQ..G...LLGVIPERRQP
Retrocopy <KAEATEFDKRDHMWICPTNLSTYQMRARGLSTEARPAESCRTSETEEPSTSQVSGEDVLLGVIPERRQP

Parental  DYLRPEMSPGSDSVPDLEEAEASVFVGQDPLPALGPAGSLGVKGAVQPQEDT-VVDAVPSFTHILE-RDL
          DYLRPE...G.DSVPD.EE.EASVFVGQDP.P.L.PAGSL.VK..V.PQEDT...DAV.SFTHILE.RDL
Retrocopy DYLRPE*GLGNDSVPDWEEGEASVFVGQDPHPTLCPAGSLRVKHVVLPQEDT<FLDAVLSFTHILE<RDL

Parental  ALNRDLQSL-SGFNL-PTSQGVASYMGNTEDGLEAANPEPANPQP
          .LNRDLQS..S.F.L.PTSQ.VASYMGNTEDGLEAANPEPA.P.P
Retrocopy VLNRDLQSICSCFQL>PTSQRVASYMGNTEDGLEAANPEPASPRP

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	0.05 RPM	0.00 RPM
SRP007412_cerebellum	0.09 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.02 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.05 RPM	3.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1078 was not detected

EST

No EST(s) were mapped for retro_mmus_1078 retrocopy.

TSS

No TSS is located nearby retro_mmus_1078 retrocopy 5' end.

Lab

retro_mmus_1078 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1078 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047236	1 retrocopy	retro_btau_975,
Myotis lucifugus	ENSMLUG00000012011	1 retrocopy	retro_mluc_30,
Mus musculus	ENSMUSG00000058028	3 retrocopies	retro_mmus_1078 , retro_mmus_1953, retro_mmus_2723,