RetrogeneDB ID: retro_ocun_561

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:54478861..54479335(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB3
• Ensembl ID: ENSOCUG00000002598
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 3 [Source:HGNC Symbol;Acc:9540]

Sequence

>retro_ocun_561
GGAGACTGGCTATAAATTGTTCTGTCTGGGCTCATCACCAATGTCCACACATGTGTACATTGCCTCAAGTTCTCATTGAA
ATCCATGGGTTGAATGAAGGTCGGCAGATCAAGCCTTATATACTGAAGAGTATGGTGGCCAAAGTCGTGTATGAGAAGCA
GTTTGGCCCCTACTCCACTGAGCCAGGCATTGCTGAGAAGGACCTGCAGACCTTTAGGCACTTCTAGTCTGGAGACCTCA
TCTACTGCCCCACGATGACCAATGACATTTTGCTGCTGGCACCTGTGCTAAACAAATACACGGGATGTGTGATTCCTTCT
GGGATCCCTTCAAATATTTATAACACTTGTTTAAACCATCTCCAAAGTCATACTGAATGCTGTGGGCCAGGATGCAGTGT
CAGGCATGCAAGTCATTGCTCCCATCTTTGAAAAGGACAAAATCAACAGCTGGCCACTGAAGGCCCTGATGGAA

Alignment

ORF - retro_ocun_561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.21 %
• Parental protein coverage: 78.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GDRLYIGLAGLATDVQTVAQRLKFRLN-LYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDP
          GD.L.I.L.GL.T.V.T....LKF.L.....L.EGRQIKPY.L.SMVA...YEK.FGPY.TEP.IA..D.
Retrocopy GDWL*IVLSGLITNVHTCVHCLKFSLK<IHGLNEGRQIKPYILKSMVAKVVYEKQFGPYSTEPGIAEKDL

Parental  KTYKPFICSLDLIGCPMVTDDFVV-SGTCAEQMYGMCESLWEPNMDPEHLFE-TISQAMLNAVDRDAVSG
          .T...F..S.DLI.CP..T.D.....GTCA.Q..GMC.S.W.P.....HLF..TIS...LNAV..DAVSG
Retrocopy QTFRHF-*SGDLIYCPTMTNDILL<AGTCAKQIHGMCDSFWDPFKYL*HLFK<TISKVILNAVGQDAVSG

Parental  MGVIVHIIEKDKITTRTLKARMD
          M.VI..I.EKDKI....LKA.M.
Retrocopy MQVIAPIFEKDKINSWPLKALME

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	31.18 RPM
SRP017611_kidney	0.00 RPM	37.50 RPM
SRP017611_liver	0.00 RPM	20.42 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_561 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_561 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016587	2 retrocopies	retro_cfam_135, retro_cfam_532,
Callithrix jacchus	ENSCJAG00000008246	1 retrocopy	retro_cjac_2852,
Equus caballus	ENSECAG00000000987	1 retrocopy	retro_ecab_476,
Erinaceus europaeus	ENSEEUG00000015275	1 retrocopy	retro_eeur_10,
Homo sapiens	ENSG00000108294	2 retrocopies	retro_hsap_1121, retro_hsap_2387,
Gorilla gorilla	ENSGGOG00000007067	2 retrocopies	retro_ggor_103, retro_ggor_876,
Loxodonta africana	ENSLAFG00000002233	1 retrocopy	retro_lafr_70,
Macropus eugenii	ENSMEUG00000004131	2 retrocopies	retro_meug_1804, retro_meug_551,
Microcebus murinus	ENSMICG00000002997	1 retrocopy	retro_mmur_397,
Macaca mulatta	ENSMMUG00000012363	1 retrocopy	retro_mmul_868,
Monodelphis domestica	ENSMODG00000012614	2 retrocopies	retro_mdom_1722, retro_mdom_1812,
Mus musculus	ENSMUSG00000069744	8 retrocopies	retro_mmus_1449, retro_mmus_1551, retro_mmus_1790, retro_mmus_1938, retro_mmus_2110, retro_mmus_41, retro_mmus_46, retro_mmus_536,
Nomascus leucogenys	ENSNLEG00000000594	3 retrocopies	retro_nleu_1511, retro_nleu_188, retro_nleu_371,
Oryctolagus cuniculus	ENSOCUG00000002598	1 retrocopy	retro_ocun_561 ,
Pongo abelii	ENSPPYG00000008505	2 retrocopies	retro_pabe_2153, retro_pabe_927,
Pteropus vampyrus	ENSPVAG00000002270	1 retrocopy	retro_pvam_822,
Rattus norvegicus	ENSRNOG00000012938	7 retrocopies	retro_rnor_1016, retro_rnor_2094, retro_rnor_2448, retro_rnor_2537, retro_rnor_2804, retro_rnor_743, retro_rnor_8,
Ictidomys tridecemlineatus	ENSSTOG00000014258	3 retrocopies	retro_itri_527, retro_itri_935, retro_itri_936,