RetrogeneDB ID: retro_ocun_595

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:13150483..13151087(+)
• Located in intron of: ENSOCUG00000006463

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_595
CACACACTCTTTCTCTCCCAGCACAGTCTCACGGCAACGATCCATACTGAAATGGCGTGGGCCGCAAGAACAATGCAGCT
TGCTGAGGTGTATCACAAGCTGATTTCATCAGTTGACCCGCAGTTCCTGAAACTCACCAAAGCGGATGACCAAATCTACT
CTGAGTTCCGAAAAATTTTTTGAGAAACTCAAGATGGATGTATTAGATCCAGGAGAACTCAAATCAGATTCTACAAAAGA
GAAGTGAAGGCCATTCTGCTTGAAGTTGGAAGGGATCGTGGAAGACTGCAACTATGGTACTCTGCTGCGACTAGATTGCT
CTCAGGGTTCCACTGAGGAGAACACCATCCTCACCCCCAGAATACAGTTTTGGGCCTTTGAGACCGCTTGGAGCCGGGAA
GGCTATAACAAAGCAGTTAACGTCGGCGCTCAGCACAAAGGAGGAGAGAAAACAGTGTCAGTGCAGGAGGGCAAGAGAAA
GCGAGAAAAAAGAAGAGAAAGGAGCCAACAGTGGCGGGAAAAAGAGGAGGGGTTTGCCGGAGAGGGCGAAAAGGAGGAAA
ATGCCAAAGAAGGAGAAAAAGAGAAAGAAGCCGACAAAGAAATC

Alignment

ORF - retro_ocun_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.21 %
• Parental protein coverage: 91.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HALSLPAESYGNDPDIEMAWAARAMQHAEVYYKLISSVDPQFLKLTKVDDQIYSEFRKIF-EKLKIDVLD
          H.L.L...S.......EMAWAAR.MQ.AEVY.KLISSVDPQFLKLTK.DDQIYSEFRKIF.EKLK.DVLD
Retrocopy HTLFLSQHSLTATIHTEMAWAARTMQLAEVYHKLISSVDPQFLKLTKADDQIYSEFRKIF>EKLKMDVLD

Parental  PEELKSESAKETWRPFCLKFEGIVEDFNYGTLLRLDCSQGYTEENTIFAPRIQFLAIEIARNREGYNKAV
          P.ELKS.S.KE..RPFCLK.EGIVED.NYGTLLRLDCSQG.TEENTI..PRIQF.A.E.A..REGYNKAV
Retrocopy PGELKSDSTKEK*RPFCLKLEGIVEDCNYGTLLRLDCSQGSTEENTILTPRIQFWAFETAWSREGYNKAV

Parental  YVGAQHKEGERA-GVSGAEQEK-PEKKEEEGANSGGK-KEEGVAGEGEKEEKAKEGEKEKEADKGI
          .VGAQHK.GE....VS...QEK..EKKEE.GANSGGK.KEEG.AGEGEKEE.AKEGEKEKEADK.I
Retrocopy NVGAQHKGGEKT<SVSAGGQEK<SEKKEEKGANSGGK<KEEGFAGEGEKEENAKEGEKEKEADKEI

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	0.11 RPM	6.46 RPM
SRP017611_kidney	0.00 RPM	4.16 RPM
SRP017611_liver	0.00 RPM	2.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_595 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_595 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,