RetrogeneDB ID: retro_ocun_1603

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018710:3363194..3363568(-)
• Located in intron of: ENSOCUG00000014076

Retrocopy information

• Ensembl ID: ENSOCUG00000015966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000013044
• Aliases: None
• Description: DNA-directed RNA polymerase subunit [Source:UniProtKB/TrEMBL;Acc:G1TAL1]

Sequence

>retro_ocun_1603
GTGGAACCGGACAGGACCTACGAGTCTGGATTCGTGGGCATTCGATTCTGCCAGGAACGTAACAACATGCTGTACCCCGA
GGAAGATAAGGAAAACCGCATTCTGCTGTACGTGTGCCGGAACTGTGATTACCAGCAGGAAGCCGACAACAGCTGCATCT
ACGTCAACAAAATCACGCACGAAGTGGACGAGCTGACCCAGATCATCGCCGACGTGTCCCAGGACCCCACGCTATCGTGG
ACCGAGGACCACCCGTGCCAGAAGTGCGGCCACAAGGAGGCGGTGTTCTTCAGTCCCACAGCGCTCGGGCCGAGGACGCC
ATGCGCCTGTACTATGAATGCACGGCCCCACACTGTGGCCACCGTTGGACCGAG

Alignment

ORF - retro_ocun_1603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIA
          .EPD.TYE.GFVGIRFCQE.NNMLYP.EDKENRILLY.CRNCDYQQEADNSCIYVNKITHEVDELTQIIA
Retrocopy VEPDRTYESGFVGIRFCQERNNMLYPEEDKENRILLYVCRNCDYQQEADNSCIYVNKITHEVDELTQIIA

Parental  DVSQDPTLPRTEDHPCQKCGHKEAVFF-QSHSARAEDAMRLYYVCTAPHCGHRWTE
          DVSQDPTL..TEDHPCQKCGHKEAVFF.QSHSARAEDAMRLYY.CTAPHCGHRWTE
Retrocopy DVSQDPTLSWTEDHPCQKCGHKEAVFF<QSHSARAEDAMRLYYECTAPHCGHRWTE

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	3.97 RPM
SRP017611_kidney	0.00 RPM	7.20 RPM
SRP017611_liver	0.00 RPM	2.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1603 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1603 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1603 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006601	1 retrocopy	retro_cfam_1400,
Callithrix jacchus	ENSCJAG00000009671	1 retrocopy	retro_cjac_2777,
Dipodomys ordii	ENSDORG00000001852	2 retrocopies	retro_dord_264, retro_dord_555,
Monodelphis domestica	ENSMODG00000014172	1 retrocopy	retro_mdom_1465,
Mus musculus	ENSMUSG00000019738	1 retrocopy	retro_mmus_2287,
Oryctolagus cuniculus	ENSOCUG00000013044	2 retrocopies	retro_ocun_103, retro_ocun_1603 ,
Otolemur garnettii	ENSOGAG00000024254	1 retrocopy	retro_ogar_386,
Ochotona princeps	ENSOPRG00000001789	2 retrocopies	retro_opri_350, retro_opri_837,
Tursiops truncatus	ENSTTRG00000003919	1 retrocopy	retro_ttru_223,