RetrogeneDB ID: retro_ocun_1017

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 19:16589446..16589842(-)
• Located in intron of: ENSOCUG00000000075

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBDC1
• Ensembl ID: ENSOCUG00000001088
• Aliases: None
• Description: polysaccharide biosynthesis domain containing 1 [Source:HGNC Symbol;Acc:28790]

Sequence

>retro_ocun_1017
AAAAAATTTGAGAAACTCAAGGTAGAAGTATTGGACCCAGAACAACTCAAGTCAGAACCGGCAGAAGAGAAGTAGAGACC
ATTCTCCTTGAAGTTGGAAGGGATTGTGGAAGACTTGACTATGGTCCTTTGCTGCAACTAGATCGTTCTCAGGGTTACAC
TGAGGAAAACACCATGTTTGCCCCCAGAATAGTTTTTGGCTACTGAAGTCGCTCAGAACCAGGAAGGTTGTAACAAGGAA
GTTTAGTTGGTGTTCAGCACAGAGAATGAGAGAAAGCAGGGGTCAGTGGAGGACAGCAAGAGAAAGCCGAGAGACAAAGG
AGAGAAAGGAGCCAACAGTGGAGGAGAAGTGGAGGGAGCTGCTGGAGAAGGAGAAAGAGAAAGAAGCGACAAAGAA

Alignment

ORF - retro_ocun_1017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.31 %
• Parental protein coverage: 60.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KIFEKLKIDVLDPEELKSESAKETWRPFCLKFEGIVED-FNYGTLLRLDCSQGYTEENTIFAPRI-QFLA
          K.FEKLK..VLDPE.LKSE.A.E..RPF.LK.EGIVED...YG.LL.LD.SQGYTEENT.FAPRI..F..
Retrocopy KKFEKLKVEVLDPEQLKSEPAEEK*RPFSLKLEGIVED<LDYGPLLQLDRSQGYTEENTMFAPRI<SFWL

Parental  IEIARNRE-GYNKAV-YVGAQHKEGERAGVSGAEQE-KPEKKEEEGANSGGKKEEGVAGEGEKEEKAKE
          ....R.R..G.NK.V..VG.QH.E.E.AGVSG..QE.KP..K.E.GANSGG...EG.AGEGE.E...KE
Retrocopy LKSLRTRK<GCNKEV<LVGVQHRE*EKAGVSGGQQE>KPRDKGEKGANSGG-EVEGAAGEGERERSDKE

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	0.77 RPM	6.46 RPM
SRP017611_kidney	0.30 RPM	4.16 RPM
SRP017611_liver	0.31 RPM	2.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1017 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1017 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1017 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002, retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017 , retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448, retro_tbel_494, retro_tbel_979,