RetrogeneDB ID: retro_ocun_1252

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:27337450..27337984(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000011908
• Aliases: None
• Description: None

Sequence

>retro_ocun_1252
ATGCCGGCATATCACTCTTCTTTCATGGACCCTGACACCAAGCTCATCGGAAACATGGCACTGTTACCTATTAGAAGTCA
GTTCAAAGGCCCTGCCCCTAGAGAGACAAAAGATACAGATATTGTGGATGAAGCCATCTATTACTTCAAGGCCAATGTCT
TCTTCAAAAACTATGAAATTAAGAATGAAGCCGACAGGACCCTGATATATATAATTCTCTACATCTCTGAGTATCTGAAG
AAACTCCAAAAGTGCAATTCCAAAAGCCAAGGCAAGAAAGAAATGTATACACTGGGAATCACAAATTTTCCGATTCCTGG
AGAGCCAGGGTTTCCACTTAATGCAATTTATGCCAAACCTGCAAACAAGTAGGAAGATGAGGTGATGCACGCCTACTTAC
AGCAGCTAAGGCAGGAGACTGGACTGAGACTTTGTGAGAAAGTTTTTGACCCTCAGAATGATAAGCCCAGCAAGTGGTGG
ACTTGCTTTGTGAAGAGACAGTTCATGAACAAGAGCCACTCGGGACCGGGGCAG

Alignment

ORF - retro_ocun_1252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY
          ..AYHSS.MDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY
Retrocopy MPAYHSSFMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY

Parental  ITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQET
          I.LYISE.LKKLQKCNSKSQG.KEMYTLGITNFPIPGEPGFPLNAIYAKPANK.EDEVM.AYLQQLRQET
Retrocopy IILYISEYLKKLQKCNSKSQGKKEMYTLGITNFPIPGEPGFPLNAIYAKPANK*EDEVMHAYLQQLRQET

Parental  GLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ
          GLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKS.SGPGQ
Retrocopy GLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSHSGPGQ

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	69.70 RPM
SRP017611_kidney	0.10 RPM	58.38 RPM
SRP017611_liver	0.00 RPM	20.81 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1252 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1252 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1252 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Dasypus novemcinctus	ENSDNOG00000004987	2 retrocopies	retro_dnov_2619, retro_dnov_685,
Dipodomys ordii	ENSDORG00000008212	1 retrocopy	retro_dord_312,
Erinaceus europaeus	ENSEEUG00000011531	2 retrocopies	retro_eeur_122, retro_eeur_99,
Echinops telfairi	ENSETEG00000006992	2 retrocopies	retro_etel_116, retro_etel_1323,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Homo sapiens	ENSG00000111229	5 retrocopies	retro_hsap_2431, retro_hsap_303, retro_hsap_3425, retro_hsap_892, retro_hsap_918,
Loxodonta africana	ENSLAFG00000006166	3 retrocopies	retro_lafr_1119, retro_lafr_763, retro_lafr_840,
Microcebus murinus	ENSMICG00000005485	2 retrocopies	retro_mmur_1009, retro_mmur_1507,
Macaca mulatta	ENSMMUG00000006492	3 retrocopies	retro_mmul_1105, retro_mmul_1174, retro_mmul_543,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Mustela putorius furo	ENSMPUG00000002151	2 retrocopies	retro_mputfur_1346, retro_mputfur_1540,
Nomascus leucogenys	ENSNLEG00000002802	4 retrocopies	retro_nleu_239, retro_nleu_283, retro_nleu_3078, retro_nleu_389,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252 ,
Otolemur garnettii	ENSOGAG00000013424	1 retrocopy	retro_ogar_2855,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Procavia capensis	ENSPCAG00000011858	2 retrocopies	retro_pcap_421, retro_pcap_441,
Pongo abelii	ENSPPYG00000004947	6 retrocopies	retro_pabe_1735, retro_pabe_1790, retro_pabe_2838, retro_pabe_376, retro_pabe_769, retro_pabe_792,
Sorex araneus	ENSSARG00000000546	2 retrocopies	retro_sara_529, retro_sara_601,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Sus scrofa	ENSSSCG00000009821	1 retrocopy	retro_sscr_177,
Ictidomys tridecemlineatus	ENSSTOG00000011979	1 retrocopy	retro_itri_1350,
Tupaia belangeri	ENSTBEG00000011219	1 retrocopy	retro_tbel_2268,
Tarsius syrichta	ENSTSYG00000002953	4 retrocopies	retro_tsyr_1150, retro_tsyr_1341, retro_tsyr_2103, retro_tsyr_794,
Tursiops truncatus	ENSTTRG00000015083	2 retrocopies	retro_ttru_713, retro_ttru_880,
Vicugna pacos	ENSVPAG00000008404	1 retrocopy	retro_vpac_225,