RetrogeneDB ID: retro_mmus_2632

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:21952406..21953026(-)
• Located in intron of: ENSMUSG00000042453

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dnaja4
• Ensembl ID: ENSMUSG00000032285
• Aliases: Dnaja4, 1110021L12Rik, AV358213, Dj4, Hsj4, mmDjA4
• Description: DnaJ (Hsp40) homolog, subfamily A, member 4 [Source:MGI Symbol;Acc:MGI:1927638]

Sequence

>retro_mmus_2632
TTAGTGAAAGAAACCGCTTATTATGATGTTTTGGGAGTTAAACCCAATACCACCCAGGAAGAACTGGAAAAGGCATATAG
AAAACTGGCCTTGAAGTAGCACCCTGATAAGAATTCAAATGAAGAAGAAAAGTATAAACAGATTTCTCAAGCTTATGAAG
TTCTTGCTGATTCCAAAAAAGGGTGGGACGGGATTATATGATAACGAGGGCATGCAGGTGATTAAAGAGGGCGGAGCAGG
TGGTGGTTTTGGCTCACCTGTGGATATCTCTGATATGTCCTTTGGAGGAAGAAGAAGAATGCAAAGAGAAAGGAGAGGTA
AAATGTTGTACATCAGCTCTCAGTGACCTTAGAAGACTTATATGATGGTGCAACAAGAAAACTGGTTCTACACAATGATA
TGATTTGTGACAAATATGAAGGCCAAGGTGACAAAGGAGCAGTAGAGTGCTGTTCCAACTGCTGGGGGACAGGTATGCAG
ATAAGGATTCATCAGATTGGACCAGGAATGGTTTAGCAAATTCAGTCATATGCATGGAGTGCCAGGGTCATGAAGAACGC
ATCAGTCCAAAAGACAGACGTAAAAGCTGCAATGGAAGAAAGATAGTTCATATTGATAAA

Alignment

ORF - retro_mmus_2632 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVKETQYYDILGVKPSASPEEIKKAYRKLALKYHPDKNPDEGEKFKLISQAYEVLSD-PKK--RDIYDQG
          .VKET.YYD.LGVKP....EE..KAYRKLALK.HPDKN..E.EK.K.ISQAYEVL.D.PKK.....YD..
Retrocopy LVKETAYYDVLGVKPNTTQEELEKAYRKLALK*HPDKNSNEEEKYKQISQAYEVLAD>PKKGGTGLYDNE

Parental  GEQAIKEGGSGSPSFSSPMDIFDMFFGGGGRMTRERRGK-NVVHQLSVTLEDLYNGITKKLALQKNVICE
          G.Q.IKEGG.G...F.SP.DI.DM.FGG..RM.RERRGK.NVVHQLSVTLEDLY.G.T.KL.L....IC.
Retrocopy GMQVIKEGGAGG-GFGSPVDISDMSFGGRRRMQRERRGK<NVVHQLSVTLEDLYDGATRKLVLHNDMICD

Parental  KCEGIGGKKGSVEKCPLCKGRGMQVHIQQIGPGMVQQIQT-VCIECKGQGERINPKDRCENCSGAKVTRE
          K.EG..G.KG.VE.C..C.G.GMQ..I.QIGPGMV.QIQ...C.EC.G..ERI.PKDR...C.G.K....
Retrocopy KYEG-QGDKGAVECCSNCWGTGMQIRIHQIGPGMV*QIQS<ICMECQGHEERISPKDRRKSCNGRKIVHI

Parental  KK
          .K
Retrocopy DK

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	22.45 RPM
SRP007412_cerebellum	0.04 RPM	26.18 RPM
SRP007412_heart	0.00 RPM	64.66 RPM
SRP007412_kidney	0.06 RPM	43.85 RPM
SRP007412_liver	0.03 RPM	6.28 RPM
SRP007412_testis	0.32 RPM	279.88 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2632 was not detected

EST

No EST(s) were mapped for retro_mmus_2632 retrocopy.

TSS

No TSS is located nearby retro_mmus_2632 retrocopy 5' end.

Lab

retro_mmus_2632 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2632 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012576	1 retrocopy	retro_amel_1659,
Dipodomys ordii	ENSDORG00000005972	4 retrocopies	retro_dord_245, retro_dord_280, retro_dord_333, retro_dord_533,
Echinops telfairi	ENSETEG00000004320	4 retrocopies	retro_etel_1010, retro_etel_1031, retro_etel_1067, retro_etel_608,
Macropus eugenii	ENSMEUG00000015982	4 retrocopies	retro_meug_1059, retro_meug_1893, retro_meug_292, retro_meug_624,
Microcebus murinus	ENSMICG00000008789	6 retrocopies	retro_mmur_1242, retro_mmur_1460, retro_mmur_39, retro_mmur_482, retro_mmur_496, retro_mmur_578,
Mus musculus	ENSMUSG00000028410	3 retrocopies	retro_mmus_2561, retro_mmus_2982, retro_mmus_3507,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632 ,
Otolemur garnettii	ENSOGAG00000006752	5 retrocopies	retro_ogar_1760, retro_ogar_1985, retro_ogar_221, retro_ogar_2656, retro_ogar_841,
Ochotona princeps	ENSOPRG00000007594	1 retrocopy	retro_opri_1028,
Tupaia belangeri	ENSTBEG00000009268	9 retrocopies	retro_tbel_2276, retro_tbel_2308, retro_tbel_2790, retro_tbel_2831, retro_tbel_3242, retro_tbel_4322, retro_tbel_4735, retro_tbel_772, retro_tbel_796,
Tarsius syrichta	ENSTSYG00000008600	1 retrocopy	retro_tsyr_1752,