RetrogeneDB ID: retro_mmus_3554

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:157663597..157663924(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083117
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dnajc19
• Ensembl ID: ENSMUSG00000027679
• Aliases: Dnajc19, 1810055D05Rik, AA959924, Tim14
• Description: DnaJ (Hsp40) homolog, subfamily C, member 19 [Source:MGI Symbol;Acc:MGI:1914963]

Sequence

>retro_mmus_3554
GTGGTAGCTGTTGGACTGACCACTGATGCTGCAGGATTTTGCAGGCCATTATATTTCACAAGCCATGAAACATGTGAAAT
AAGTTAAACAGTTTTCCAAAATCTACCAACATCTGCCTTCAGGGGTGGGAAGTACAGAGCTGGTTTTGAACCCACAATGC
CAGAGCAGAATGTAGCATTCATGCTTGGTGGGATCCCTACTTCCAAGAAAGGGAAGATTAGATGTGATCGTGGATGAATT
ATGTACCGAAATCATCCAGACAATGGAGGATCTCCTTATATAGCAGCCAGCATCAATGTAGTTAAAGACCCACTACAAGG
TCAAGCT

Alignment

ORF - retro_mmus_3554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 94.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVAVGLTIAAAGF-AGRYVLQAMKHVEPQVKQ-VFQSLPKSAFGGGYYRGGFEPKMTKREAALILGVSPT
          VVAVGLT..AAGF.AG.Y..QAMKHV...VKQ.VFQ.LP.SAF.GG.YR.GFEP.M.....A..LG..PT
Retrocopy VVAVGLTTDAAGF>AGHYISQAMKHVK*-VKQ<VFQNLPTSAFRGGKYRAGFEPTMPEQNVAFMLGGIPT

Parental  ANKGKIRDAHRRIMLLNHPDKGGSPYIAAKINEAKDLLEGQA
          ..KGKIR.....IM..NHPD.GGSPYIAA.IN..KD.L.GQA
Retrocopy SKKGKIRCDRG*IMYRNHPDNGGSPYIAASINVVKDPLQGQA

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	10.37 RPM
SRP007412_cerebellum	0.00 RPM	9.21 RPM
SRP007412_heart	0.00 RPM	18.52 RPM
SRP007412_kidney	0.00 RPM	29.76 RPM
SRP007412_liver	0.00 RPM	19.80 RPM
SRP007412_testis	0.00 RPM	8.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3554 was not detected

EST

No EST(s) were mapped for retro_mmus_3554 retrocopy.

TSS

No TSS is located nearby retro_mmus_3554 retrocopy 5' end.

Lab

retro_mmus_3554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3554 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 93 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023513	1 retrocopy	retro_btau_127,
Callithrix jacchus	ENSCJAG00000012795	10 retrocopies	retro_cjac_1008, retro_cjac_1192, retro_cjac_1364, retro_cjac_1430, retro_cjac_1550, retro_cjac_252, retro_cjac_2609, retro_cjac_2890, retro_cjac_3060, retro_cjac_914,
Cavia porcellus	ENSCPOG00000021198	1 retrocopy	retro_cpor_126,
Dasypus novemcinctus	ENSDNOG00000019067	1 retrocopy	retro_dnov_49,
Erinaceus europaeus	ENSEEUG00000006955	9 retrocopies	retro_eeur_221, retro_eeur_230, retro_eeur_309, retro_eeur_455, retro_eeur_48, retro_eeur_511, retro_eeur_596, retro_eeur_74, retro_eeur_94,
Echinops telfairi	ENSETEG00000006897	7 retrocopies	retro_etel_1071, retro_etel_1222, retro_etel_1559, retro_etel_275, retro_etel_384, retro_etel_81, retro_etel_821,
Ficedula albicollis	ENSFALG00000008296	1 retrocopy	retro_falb_28,
Gallus gallus	ENSGALG00000008852	1 retrocopy	retro_ggal_17,
Loxodonta africana	ENSLAFG00000001910	5 retrocopies	retro_lafr_48, retro_lafr_515, retro_lafr_611, retro_lafr_881, retro_lafr_929,
Microcebus murinus	ENSMICG00000010381	4 retrocopies	retro_mmur_1160, retro_mmur_225, retro_mmur_320, retro_mmur_728,
Myotis lucifugus	ENSMLUG00000006865	1 retrocopy	retro_mluc_84,
Mus musculus	ENSMUSG00000027679	3 retrocopies	retro_mmus_1446, retro_mmus_3071, retro_mmus_3554 ,
Otolemur garnettii	ENSOGAG00000008754	11 retrocopies	retro_ogar_1214, retro_ogar_1334, retro_ogar_138, retro_ogar_1625, retro_ogar_1811, retro_ogar_2012, retro_ogar_2048, retro_ogar_2881, retro_ogar_301, retro_ogar_442, retro_ogar_718,
Ochotona princeps	ENSOPRG00000009256	5 retrocopies	retro_opri_1127, retro_opri_122, retro_opri_440, retro_opri_529, retro_opri_844,
Procavia capensis	ENSPCAG00000014950	2 retrocopies	retro_pcap_195, retro_pcap_25,
Pongo abelii	ENSPPYG00000014328	2 retrocopies	retro_pabe_2126, retro_pabe_44,
Rattus norvegicus	ENSRNOG00000049819	1 retrocopy	retro_rnor_2913,
Ictidomys tridecemlineatus	ENSSTOG00000011508	1 retrocopy	retro_itri_552,
Tupaia belangeri	ENSTBEG00000015089	27 retrocopies	retro_tbel_1126, retro_tbel_1166, retro_tbel_1167, retro_tbel_1296, retro_tbel_1301, retro_tbel_1491, retro_tbel_1693, retro_tbel_1780, retro_tbel_2117, retro_tbel_2136, retro_tbel_2267, retro_tbel_2459, retro_tbel_266, retro_tbel_2830, retro_tbel_3233, retro_tbel_3303, retro_tbel_3556, retro_tbel_3716, retro_tbel_3814, retro_tbel_384, retro_tbel_3849, retro_tbel_3963, retro_tbel_4043, retro_tbel_42, retro_tbel_633, retro_tbel_833, retro_tbel_889,