RetrogeneDB ID: retro_mmus_1433

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:8612970..8613408(+)
• Located in intron of: ENSMUSG00000057880

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zmynd19
• Ensembl ID: ENSMUSG00000026974
• Aliases: None
• Description: zinc finger, MYND domain containing 19 [Source:MGI Symbol;Acc:MGI:1914437]

Sequence

>retro_mmus_1433
AAAAACAAACAGGACTTGAGTGGGCTTCTCTATGAGATCCTGTGGGAACCACACAGGGAGGCATGGCCCACTGGTTTCAG
GTAGAGCATCTCAATATTGTGACAGAGGATGTTTGCCTGGAAAACCTGCAGTTGATGCTGTGGAACCGGCAGACCAAAGC
TAAAGAGACCTCCAGTAACAAGGGAGCAAAGCTTATACTGGCTGGCAACCCAGCAGCTTTCCACGGACCCCAGAGAAGAG
CAGTCCCCTCTCCTGGATGTGACTCAGCACCGCAGTGCCAGTGGGGTGTGGTGGAGGAGAATTCCTGGAGCCATTCTGAG
TGTCATCATGTTCCCTGCAGTGAGACTGAGAAGCAGCTTCCCAAGATCAGCCTTTGTGGATGCTGCCAGGTGGCCTGGGA
CCATGGGTCCCAGGTGCCAGCAGCAGGATTGGATTGCC

Alignment

ORF - retro_mmus_1433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.49 %
• Parental protein coverage: 66.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KNRGRGSGRLLHELLWERHR-GGVAPGFQVVHLNAVTVDNRLDNLQLVPWG-WRPKAEETSSKQREQSLY
          KN....SG.LL.E.LWE.HR.GG.A..FQV.HLN.VT.D..L.NLQL..W...RPK........REQSLY
Retrocopy KNKQDLSG-LLYEILWEPHR<GGMAHWFQVEHLNIVTEDVCLENLQLMLWN>GRPKLKRPPVT-REQSLY

Parental  WLAIQQLPTDPIEEQFPVLNVTRYYNANG-DVVEEEENSCTYYECHYPPCTVIEKQLREFNICGRCQVAR
          WLA.QQL.TDP.EEQ.P.L.VT....A.G..VVE..ENS....ECH..PC...EKQL.....CG.CQVA.
Retrocopy WLATQQLSTDPREEQSPLLDVTQHRSASG<GVVE--ENSWSHSECHHVPCSETEKQLPKISLCGCCQVAW

Parental  YCGSQ-CQQKDWPA
          ..GSQ.CQQ.DW.A
Retrocopy DHGSQ>CQQQDWIA

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	0.86 RPM	21.56 RPM
SRP007412_cerebellum	0.43 RPM	20.10 RPM
SRP007412_heart	0.00 RPM	12.79 RPM
SRP007412_kidney	0.21 RPM	10.30 RPM
SRP007412_liver	0.16 RPM	11.41 RPM
SRP007412_testis	0.14 RPM	44.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1433 was not detected

EST

No EST(s) were mapped for retro_mmus_1433 retrocopy.

TSS

No TSS is located nearby retro_mmus_1433 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: GCTAGAGGAGAGATACTCGT (20 nt long)
• Reverse primer: GAGCACTGGAGATAGAGTCC (20 nt long)
• Anneling temperature: 55 °C
• (Expected) product size: 732
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1433 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006644	2 retrocopies	retro_dnov_1389, retro_dnov_1468,
Dipodomys ordii	ENSDORG00000008360	1 retrocopy	retro_dord_390,
Equus caballus	ENSECAG00000012412	1 retrocopy	retro_ecab_903,
Echinops telfairi	ENSETEG00000005023	1 retrocopy	retro_etel_1068,
Homo sapiens	ENSG00000165724	1 retrocopy	retro_hsap_1367,
Gorilla gorilla	ENSGGOG00000006875	1 retrocopy	retro_ggor_1065,
Macropus eugenii	ENSMEUG00000011727	1 retrocopy	retro_meug_2010,
Macaca mulatta	ENSMMUG00000019610	1 retrocopy	retro_mmul_2195,
Monodelphis domestica	ENSMODG00000017172	1 retrocopy	retro_mdom_764,
Mus musculus	ENSMUSG00000026974	3 retrocopies	retro_mmus_1433 , retro_mmus_2466, retro_mmus_942,
Nomascus leucogenys	ENSNLEG00000009236	1 retrocopy	retro_nleu_1071,
Tursiops truncatus	ENSTTRG00000010812	1 retrocopy	retro_ttru_900,