RetrogeneDB ID: retro_ocun_1341

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:4349463..4349871(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSOCUG00000005194
• Aliases: None
• Description: thioesterase superfamily member 4 [Source:HGNC Symbol;Acc:17947]

Sequence

>retro_ocun_1341
ACAAAGTTTGTGGAAGAACAAACGCCAAAGGCTCAGATCTTCACAAGAAGCCTTGAGGAAGGCCTGGGCTTCGAATATGT
GATGTTCCATAATGAAGCTGAGAAAAGAGTAGTTTGTGTTTTCCAAGGAGGTCCTCATCTGCAAGGAAACTATGGATACG
TTCATGGAGGTGCCATTGCAACCATGATTGATATTACAGCTGGTACATGTACAGTTTTAACTGGAGGATATGCCATGACT
GCCAATCTAAACATCAATTTTAGAAGACCTATCCCCCTTTGTTCTGTTGTTGTGATAAACAGCCAAATTGATAAAATTGA
AGGAAGGAAATATTTTATTTCCTGTGATATTCGGAGTGTTGATGAGAAGACGCTTTACTCAGAGGCCACGAGCTTATTTA
TAAAGCTG

Alignment

ORF - retro_ocun_1341 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.85 %
• Parental protein coverage: 56.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKFVEEQTPKAQIFTRSLEEGLGFEYVMFHNEAEKRVVCVFQGGPHLQGNHGYVHGGAIATMIDITAGTC
          TKFVEEQTPKAQIFTRSLEEGLGFEYVMFHNEAEKRVVCVFQGGPHLQGN.GYVHGGAIATMIDITAGTC
Retrocopy TKFVEEQTPKAQIFTRSLEEGLGFEYVMFHNEAEKRVVCVFQGGPHLQGNYGYVHGGAIATMIDITAGTC

Parental  AVLTGGYAMTANLNINFRRPIPLCSVVVINSQIDKIEGRKYFISCDIRSVDEKTLYSEATTFLVKV
          .VLTGGYAMTANLNINFRRPIPLCSVVVINSQIDKIEGRKYFISCDIRSVDEKTLYSEAT....K.
Retrocopy TVLTGGYAMTANLNINFRRPIPLCSVVVINSQIDKIEGRKYFISCDIRSVDEKTLYSEATSLFIKL

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	0.55 RPM	3.15 RPM
SRP017611_kidney	5.78 RPM	5.88 RPM
SRP017611_liver	0.54 RPM	1.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1341 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1341 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1341 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341 ,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,