RetrogeneDB ID: retro_ocun_30

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018705:4354206..4354884(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000002718
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005712
• Aliases: None
• Description: None

Sequence

>retro_ocun_30
ATGGTCATGGCGGAGGGGACGGCAGTGTTGAGGCGGAACAGGCCGGGCACCAAGGCGCAGGATTTCTATAATTGGCCTGA
TGAATCCTTTGATGAAATGGACAGTACACTTGCTGTTCAGCAGTATATTCAGCAGAACATAAGAGCAGATTGCTCCAATA
TTGATAAAATTCTTGAACCACCTGAAGGCCAAGATGAAGGTGTATGGAAGTATGAACATTTAAGGCAATTCTGTCTTGAG
CTAAATGGACTTGCTGTCAAACTTCAGAGTGAATGCCATCCAGATACTTGTACTCAAATGACAGCAACTGAACAGTGGAT
TTTTCTGTGTGCAGCTCATAAAACTCCAAAAGAGTGTCCTGCTATAGACTATACTAGACACACGCTTGATGGTGCTGCAT
GTCTTCTGAATAGCAATAAATATTTTCCTAGCAGGGTTAGCATAAAGGAATCATCTGTAGCAAAACTAGGATCAGTATGC
CGTAGGATTTATAGAATATTTTCGCATGCTTATTTTCATCACCGGCAGATATTTGATGAATATGAAAATGAAACCTTTTT
GTGTCATCGGTTTACTAAATTTGTGATGAAATACAATTTGATGTCCAAGGATAACCTGATTGTACCAATTTTAGAAGAGG
AAGTTCAGAATTCAGTTTCTGGAGAAAGTGAAGCATGA

Alignment

ORF - retro_ocun_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MVMAEGTAVLRRNRPGTKAQDFYNWPDESFDEMDSTLAVQQYIQQNIRADCSNIDKILEPPEGQDEGVWK
          MVMAEGTAVLRRNRPGTKAQDFYNWPDESFDEMDSTLAVQQYIQQNIRADCSNIDKILEPPEGQDEGVWK
Retrocopy MVMAEGTAVLRRNRPGTKAQDFYNWPDESFDEMDSTLAVQQYIQQNIRADCSNIDKILEPPEGQDEGVWK

Parental  YEHLRQFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNK
          YEHLRQFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNK
Retrocopy YEHLRQFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNK

Parental  YFPSRVSIKESSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETFLCHRFTKFVMKYNLMSKDNLIVPI
          YFPSRVSIKESSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETFLCHRFTKFVMKYNLMSKDNLIVPI
Retrocopy YFPSRVSIKESSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETFLCHRFTKFVMKYNLMSKDNLIVPI

Parental  LEEEVQNSVSGESEA
          LEEEVQNSVSGESEA
Retrocopy LEEEVQNSVSGESEA

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	0.33 RPM	8.83 RPM
SRP017611_kidney	0.10 RPM	8.11 RPM
SRP017611_liver	0.00 RPM	2.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_30 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_30 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_30 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000884	5 retrocopies	retro_chof_1077, retro_chof_1354, retro_chof_1631, retro_chof_177, retro_chof_213,
Callithrix jacchus	ENSCJAG00000004020	2 retrocopies	retro_cjac_1960, retro_cjac_3238,
Cavia porcellus	ENSCPOG00000012746	2 retrocopies	retro_cpor_318, retro_cpor_804,
Dasypus novemcinctus	ENSDNOG00000008252	1 retrocopy	retro_dnov_211,
Echinops telfairi	ENSETEG00000000932	1 retrocopy	retro_etel_952,
Homo sapiens	ENSG00000115540	2 retrocopies	retro_hsap_2275, retro_hsap_906,
Gorilla gorilla	ENSGGOG00000009005	2 retrocopies	retro_ggor_733, retro_ggor_743,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Microcebus murinus	ENSMICG00000008599	1 retrocopy	retro_mmur_1280,
Macaca mulatta	ENSMMUG00000016547	1 retrocopy	retro_mmul_829,
Monodelphis domestica	ENSMODG00000012305	2 retrocopies	retro_mdom_1333, retro_mdom_963,
Nomascus leucogenys	ENSNLEG00000006881	2 retrocopies	retro_nleu_287, retro_nleu_376,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30 ,
Otolemur garnettii	ENSOGAG00000000272	1 retrocopy	retro_ogar_2739,
Ochotona princeps	ENSOPRG00000016650	2 retrocopies	retro_opri_444, retro_opri_812,
Pongo abelii	ENSPPYG00000013047	6 retrocopies	retro_pabe_1943, retro_pabe_2021, retro_pabe_3600, retro_pabe_781, retro_pabe_795, retro_pabe_970,
Pan troglodytes	ENSPTRG00000012775	3 retrocopies	retro_ptro_1609, retro_ptro_626, retro_ptro_640,
Sarcophilus harrisii	ENSSHAG00000017821	1 retrocopy	retro_shar_351,
Sus scrofa	ENSSSCG00000016079	2 retrocopies	retro_sscr_804, retro_sscr_824,
Ictidomys tridecemlineatus	ENSSTOG00000021024	1 retrocopy	retro_itri_727,
Tarsius syrichta	ENSTSYG00000001726	1 retrocopy	retro_tsyr_1673,