RetrogeneDB ID: retro_ocun_1869

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:2659464..2659810(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000010786
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJC19
• Ensembl ID: ENSOCUG00000014043
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 19 [Source:HGNC Symbol;Acc:30528]

Sequence

>retro_ocun_1869
ATGGCCAGTACAGTGGTAGCAGCTGGACTGACCGCTGCTGCCGCAGGATTTGCAGGCCGTTATGCGTTGCAAGCCATGAA
GTATATGGAGCCTCAAGTAAAACAGTTTTTCAAAGTCTACCAAAATCTGCCTTCAGTGGTGGCTATTACAGAGGTGGATT
TGAACCCAAAATGACAAAACGAGAAGCATCATTAAAACTAGGCGTAAGCCCTACTACCAATAAAGGAAAAATAAGAGATG
TGCATCGACAAATTATGCTCTTAAATCTCCCAGACAAGGGAGGACCTCCTGATACAGCAGCCAAAGCAATGAAGCTAAAG
ATTTGCTAGGAGGTCAAGCTAAAAAA

Alignment

ORF - retro_ocun_1869 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASTVVAVGLTIAAAGFAGRYVLQAMKHMEPQVKQ-VFQSLPKSAFSGGYYRGGFEPKMTKREAALILGV
          MASTVVA.GLT.AAAGFAGRY.LQAMK.MEPQVKQ.VFQSLPKSAFSGGYYRGGFEPKMTKREA.L.LGV
Retrocopy MASTVVAAGLTAAAAGFAGRYALQAMKYMEPQVKQ<VFQSLPKSAFSGGYYRGGFEPKMTKREASLKLGV

Parental  SPTANKGKIRDAHRRIMLLNHPDKGGSPYIAAKI-NEAKDLLEGQAKK
          SPT.NKGKIRD.HR.IMLLN.PDKGG.P..AAK..NEAKDLL.GQAKK
Retrocopy SPTTNKGKIRDVHRQIMLLNLPDKGGPPDTAAKA<NEAKDLLGGQAKK

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
SRP017611_brain	0.00 RPM	14.90 RPM
SRP017611_kidney	0.00 RPM	33.45 RPM
SRP017611_liver	0.00 RPM	5.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1869 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1869 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1869 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 119 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023513	1 retrocopy	retro_btau_127,
Canis familiaris	ENSCAFG00000032714	8 retrocopies	retro_cfam_1256, retro_cfam_1306, retro_cfam_1451, retro_cfam_2015, retro_cfam_346, retro_cfam_389, retro_cfam_741, retro_cfam_819,
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,
Dasypus novemcinctus	ENSDNOG00000019067	1 retrocopy	retro_dnov_49,
Dipodomys ordii	ENSDORG00000005862	7 retrocopies	retro_dord_232, retro_dord_295, retro_dord_320, retro_dord_53, retro_dord_586, retro_dord_684, retro_dord_794,
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,
Homo sapiens	ENSG00000205981	8 retrocopies	retro_hsap_1330, retro_hsap_2061, retro_hsap_2062, retro_hsap_2349, retro_hsap_3497, retro_hsap_387, retro_hsap_538, retro_hsap_583,
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,
Oryctolagus cuniculus	ENSOCUG00000001696	4 retrocopies	retro_ocun_1101, retro_ocun_487, retro_ocun_882, retro_ocun_936,
Oryctolagus cuniculus	ENSOCUG00000014043	5 retrocopies	retro_ocun_1100, retro_ocun_1650, retro_ocun_1869 , retro_ocun_334, retro_ocun_398,
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,
Pongo abelii	ENSPPYG00000014328	2 retrocopies	retro_pabe_2126, retro_pabe_44,
Pan troglodytes	ENSPTRG00000030046	7 retrocopies	retro_ptro_1374, retro_ptro_1719, retro_ptro_2370, retro_ptro_2927, retro_ptro_404, retro_ptro_429, retro_ptro_907,
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,