RetrogeneDB ID: retro_ocun_283

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:46542411..46542780(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026913
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC50A1
• Ensembl ID: ENSOCUG00000023383
• Aliases: None
• Description: solute carrier family 50 (sugar efflux transporter), member 1 [Source:HGNC Symbol;Acc:30657]

Sequence

>retro_ocun_283
GCACTACTGCCCTCAGAAGCATCCCTGCTGGGGTTCCTTCTCCTGGGCTATGCCTATTTCTGTCTCCTGGTGCCTGACCC
CAAGGCTGGGCTTTCACAGCTGGGCCTCTTCTGCAGCCTCTTCACCATCAGCATGTACCGCTCACCGCTGGCTGACCTGG
TCAGGGTCGTTCAGACTAAATCAACAAAACGTCTCTTCTTCTCACTCACAATTGTCACCCTCTTTACCTCTGCCTCCTGG
TCTCTCAATGGGTTTCAACTCCAAGATCCCTACATCATAGTGCCCAACCTTCCGGAAATCCTCACCAGCTTCTGGCTTTT
CTGGAAGTACCCACAAGAGCAAGACAGGAACTATCAGCTCCTGCAAACC

Alignment

ORF - retro_ocun_283 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 56.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVLLPTASLLGFLVLGYAYFWLLVPDPEAQLQQLGLFCSVFTISMYVSPLADLAKVIQTKSTKRLSFSLT
          A.L...ASLLGFL.LGYAYF.LLVPDP.A.L.QLGLFCS.FTISMY.SPLADL..V.QTKSTKRL.FSLT
Retrocopy ALLPSEASLLGFLLLGYAYFCLLVPDPKAGLSQLGLFCSLFTISMYRSPLADLVRVVQTKSTKRLFFSLT

Parental  IATLLTSASWSFYGFRLRDPYIMVPNLPGILTSFIRFWLFWKYPQEQDRNYRLLQT
          I.TL.TSASWS..GF.L.DPYI.VPNLP.ILTSF...WLFWKYPQEQDRNY.LLQT
Retrocopy IVTLFTSASWSLNGFQLQDPYIIVPNLPEILTSF---WLFWKYPQEQDRNYQLLQT

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	3.75 RPM
SRP017611_kidney	0.10 RPM	11.05 RPM
SRP017611_liver	0.08 RPM	10.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_283 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_283 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000023383	1 retrocopy	retro_ocun_283 ,