RetrogeneDB ID: retro_mmus_3346

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:63443168..63444075(-)
• Located in intron of: ENSMUSG00000037801

Retrocopy information

• Ensembl ID: ENSMUSG00000091866
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dnajc17
• Ensembl ID: ENSMUSG00000034278
• Aliases: Dnajc17, 1700025B16Rik, C87112, D9Bwg1371e
• Description: DnaJ (Hsp40) homolog, subfamily C, member 17 [Source:MGI Symbol;Acc:MGI:1916658]

Sequence

>retro_mmus_3346
ATGGGGGTGACCAAAGAGCTCTTACAAATGGATCTGTACGCACTGCTAGGCATTGAGGAGAAGGCGGCAGACAAAGAGGT
GAAGAAGGCGTACAGGCAAAAAGCACTGTCCTGCCACCCAGACAAAAATCCAGATAACCCCAGAGCAGCTGAACTCTTCC
ACCAGCTGTCCCAGGCCTTGGAAGTGCTGACAGATGCTGCAGCCAGGGCTGCGTATGACAAGGTTAGGAAAGCCAAGAAG
CAGGCAGCAGAGAGGACCCAGAGACTTGACAAGGACAGGAAGAAAGTGAAACTTGACCTGGAGGCCAGGGAGCGGCAGGC
CCAGGCCCAGGGGAGTGAGGAAGAGGAGGAGAGCAGGAGCGCTACCCACTAGAGCAGGAGGTTGCTCGACTTCGAGAAGA
GGGTTCCCGTCAGTTGGAAGAGCAGCAGAGGCTGATCCAGGAGCTGATCCGCCAGGACCGAGAACAGAGGCTGAGAGGAA
GAACGGAAAATACTGAAGGCAAAGGAACCCCAAACTAAAGCTAAAGTGGAAGGGCAAGAAGGAGGATGAGTCCCAAGGTG
GCTATTCCAGAGATGTCCTCCTGAGGCTTTTACAGAAGTTTGGGGAGGTTCTCAACCTGGTACTTTCCAGAAAGAAGGCA
GGCAATGCCATAGTGGAGTTTGCAACTGTCAGAGCTGCGGAGCTGGCTGTCAGAAATGAAGTGGGCCTGGCTGACAACCC
TCTGAAGGTTTCCTGGTTGGAGGGACAGTCCCAGAGCACAGTGGACCCCGGCCCCCCAGGACTGTCAAAGGGCTCAGTGC
TGTCAGAAAGGGACGATGAGAGTCTCGTCATGATGCGCATGCGCCAAGCAGCTGATCGCCAGCAGCTGATCATCCAGATG
CAGCAGGAAGATGAGGGGCGGCCCACG

Alignment

ORF - retro_mmus_3346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVTKELLQMDLYALLGIEEKAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLTDAAARA
          M.VTKELLQMDLYALLGIEEKAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLTDAAARA
Retrocopy MGVTKELLQMDLYALLGIEEKAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLTDAAARA

Parental  AYDKVRKAKKQAAERTQRLDENRKKVKLDLEARERQAQAHGSEEEEESRSAT-TLEQEIARLREEGSRQL
          AYDKVRKAKKQAAERTQRLD..RKKVKLDLEARERQAQA.GSEEEEESRSAT..LEQE.ARLREEGSRQL
Retrocopy AYDKVRKAKKQAAERTQRLDKDRKKVKLDLEARERQAQAQGSEEEEESRSAT<PLEQEVARLREEGSRQL

Parental  EEQQRLIQEQIRQDREQRLRGRTENTEGKGT-PKLKLKWKCKKEDESQGGYSRDVLLRLLQKYGEVLNLV
          EEQQRLIQE.IRQDREQRLRGRTENTEGKGT.PKLKLKWK.KKEDESQGGYSRDVLLRLLQK.GEVLNLV
Retrocopy EEQQRLIQELIRQDREQRLRGRTENTEGKGT<PKLKLKWKGKKEDESQGGYSRDVLLRLLQKFGEVLNLV

Parental  LSRKKAGNAIVEFATVRAAELAVRNEVGLADNPLKVSWLEGQPQSTVDPGPPGLSKGSVLSERDFESLVM
          LSRKKAGNAIVEFATVRAAELAVRNEVGLADNPLKVSWLEGQ.QSTVDPGPPGLSKGSVLSERD.ESLVM
Retrocopy LSRKKAGNAIVEFATVRAAELAVRNEVGLADNPLKVSWLEGQSQSTVDPGPPGLSKGSVLSERDDESLVM

Parental  MRMRQAAERQQLIAQMQQEDEGRPT
          MRM...........QMQQEDEGRPT
Retrocopy MRMXXXXXXXXXXIQMQQEDEGRPT

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	0.23 RPM	4.53 RPM
SRP007412_cerebellum	0.48 RPM	4.34 RPM
SRP007412_heart	0.03 RPM	3.27 RPM
SRP007412_kidney	0.21 RPM	2.79 RPM
SRP007412_liver	0.05 RPM	1.09 RPM
SRP007412_testis	1.05 RPM	6.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3346 was not detected

EST

No EST(s) were mapped for retro_mmus_3346 retrocopy.

TSS

No TSS is located nearby retro_mmus_3346 retrocopy 5' end.

Lab

retro_mmus_3346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3346 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346 ,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,