RetrogeneDB ID: retro_ocun_1402

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:24578917..24579310(+)
• Located in intron of: None

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_1402
AGAGCGATGCAGCATGCTGAAGTGTGTTACAAGCTGATTTCATCAGTTGACCCACAGTTCCTGAAACTCACCAAAGTGGA
TGACCAAATCTACTCTGAGTTCCAAAAAATTTTTGAGAAACTCAAGATAGATGTGTTAGACCCAGAAGAACTTAAACCAG
AATCAGCAAAAGAGAAGCGGAGGCCATTCTGCTTGAAGTTTAAAGGGATTGTGGAAGACTTCATCTATGGTACTTTGCTG
CAACTAGATTGTACTCAGAGTTACACTGAGGAAAACACCATCTTTGCTCCCAAAATACAGTTTTTGGCCATTGAAACAGC
TCGGAACCAGGAAGGCTGTAACAAAGCAGTTTACATCAGTGTTCAGCACAAAGGAGAGAAAGCAGGGGTCAGT

Alignment

ORF - retro_ocun_1402 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.48 %
• Parental protein coverage: 59.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAMQHAEVYYKLISSVDPQFLKLTKVDDQIYSEFRKIFEKLKIDVLDPEELKSESAKETWRPFCLKFEGI
          RAMQHAEV.YKLISSVDPQFLKLTKVDDQIYSEF.KIFEKLKIDVLDPEELK.ESAKE..RPFCLKF.GI
Retrocopy RAMQHAEVCYKLISSVDPQFLKLTKVDDQIYSEFQKIFEKLKIDVLDPEELKPESAKEKRRPFCLKFKGI

Parental  VEDFNYGTLLRLDCSQGYTEENTIFAPRIQFLAIEIARNREGYNKAVYVGAQHKEGERAGVS
          VEDF.YGTLL.LDC...................IE.ARN.EG.NKAVY...QHK.GE.AGVS
Retrocopy VEDFIYGTLLQLDCTXXXXXXXXXXXXXXXXXXIETARNQEGCNKAVYISVQHK-GEKAGVS

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	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_1402 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1402 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,