RetrogeneDB ID: retro_mmus_2466

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:59368305..59368864(-)
• Located in intron of: ENSMUSG00000038578

Retrocopy information

• Ensembl ID: ENSMUSG00000083979
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2466
GCCCGAATGGAAGTAGATGCTGATGGAAATGGTGCTAAGATATTTGCATATGCCTTTGACAAAAACCGAGGAAAGGGCTC
AGGCAGGCTTCTGCATGAGCTGCTGTGGGACTGGCACAGGGGAGGTGTGGCTCCCGGGTTTCAGGTGGTTTATCTCAATG
CTGTGACTGTGGACAATCACTTGGACAACCTGCCGCTGGTACCATGGGGCTGGCGACCCAAAGCTGAAGAGACCTCCAGC
AAAAAGCTTATACTGGCTTGCAATCCAGCAGCTTCCCACAGACCCTATAGAAGAACATTTCCCTGTCTTGAATGTGACCC
AGTACTATAATGCCAATGGGGATGTGGTGGAAGAGGAAGAAAATTCCTGTACCTACTATGAATGTCATTCTCCTCCTTGT
ATGGTGATTGAAAAGCAGCTTTGAGAGTTCAACATCTGTGGGGGTTGCCCGGTGGCTTGATACTGTGGCTTTCAGTGCCA
GCAGAAGGACCGGCCTGGCCACAAGAAGCACTGTCGGGAGAGGAAGTGTCCCTTCCAGCACAAGCTTGAGCCAGAACGA

Alignment

ORF - retro_mmus_2466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.29 %
• Parental protein coverage: 83.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARMEVDADGNGAKIFAYAFDKNRGRGSGRLLHELLWERHRGGVAPGFQVVHLNAVTVDNRLDNLQLVPWG
          ARMEVDADGNGAKIFAYAFDKNRG.GSGRLLHELLW..HRGGVAPGFQVV.LNAVTVDN.LDNL.LVPWG
Retrocopy ARMEVDADGNGAKIFAYAFDKNRGKGSGRLLHELLWDWHRGGVAPGFQVVYLNAVTVDNHLDNLPLVPWG

Parental  WR-PKAEETSSKQREQSLYWLAIQQLPTDPIEEQFPVLNVTRYYNANGDVVEEEENSCTYYECHYPPCTV
          WR.PK......K....SLYWLAIQQLPTDPIEE.FPVLNVT.YYNANGDVVEEEENSCTYYECH.PPC.V
Retrocopy WR>PKLKRPPAK----SLYWLAIQQLPTDPIEEHFPVLNVTQYYNANGDVVEEEENSCTYYECHSPPCMV

Parental  IEKQLREFNICGRCQVARYCGSQCQQKDWPAHKKHCRERKRPFQHELEPER
          IEKQL.EFNICG.C.VA.YCG.QCQQKD.P.HKKHCRERK.PFQH.LEPER
Retrocopy IEKQL*EFNICGGCPVA*YCGFQCQQKDRPGHKKHCRERKCPFQHKLEPER

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	21.56 RPM
SRP007412_cerebellum	0.00 RPM	20.10 RPM
SRP007412_heart	0.03 RPM	12.79 RPM
SRP007412_kidney	0.04 RPM	10.30 RPM
SRP007412_liver	0.00 RPM	11.41 RPM
SRP007412_testis	0.00 RPM	44.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2466 was not detected

EST

No EST(s) were mapped for retro_mmus_2466 retrocopy.

TSS

No TSS is located nearby retro_mmus_2466 retrocopy 5' end.

Lab

retro_mmus_2466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2466 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,