RetrogeneDB ID: retro_ocun_1778

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018888:405593..406544(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000014956
• Aliases: None
• Description: None

Sequence

>retro_ocun_1778
ATGGATGCGCTCATAGACGATGATATCTGCATTCTGAATCAGGAGAAAGCTCATGAGAGAGATCCAGTGACTCCGGTCTC
AATATATTCAGGGGATGAATCTGTCACTTCACGCTTCGCCCTTGTCATTGCATATGAGGATATCAAAAAACGCCTTAAAG
AGTCAGAGAAGGAGAACTCATTCTTAAAGAAGCGAGTAAGGTTTTTGGAAGAAAAGCTTATAGGCGCTCAGTTAGATGAA
GAGACGTATTCCGTGGGACGAGAACAACTAAATAAGGCTTATCATGCATATTGAGAGGTTTACATTGATAGAGAAATTTT
GAAGAACAACGCTGAATAAAATGAACCAAAACAACCCTGAACCTCTGAAAGCATTGAATGAACAGGTACAGTCTAAAGAA
GTAAAACGGCTTCAGCTAAGAACAGAAGTAGGAACTCAGTAGGTGATGAGAAATTCAAATCCTCCTTTAAGGAACTGGGA
ATTGGAAAAGTTGAACTGTGACCTGATGATCCATGGTTTAGAAAAAGAGCTGGAATTGGTGAGGAAAGAATGTAGCGATC
TCAAAATAGAGCTACAAAAGGCCAAACAAATGGATCCATCCGAGGAAGACAACCTGAAGAACAGTGCTCTTCGAAGAGCA
AGCATTTCAAGGGATAATATGCAACAGTGTACTGGGAACTGAAGAGGGAAATGTCTGACTTACATCTGATGACTCAAGTA
CAAGCTGAACGGCTAAGAAAACTGAAAATGCCAACTGCATTCAAGAAAGCCTGTGCCCCACTAACCTGCGCTGAAGACCT
TGGGAAAGAGCACAAAACTCCACTTGACAAATTTTACTGCATCTTATAAAAGACATGTCTGTCTATCACCAAATGGCAAA
GCTGTTTTCACACTACTTCTTCCCCTTTACCAGGAGATATAAAGATTTTATCCAAAAAAAAAAAAAAGCAG

Alignment

ORF - retro_ocun_1778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.47 %
• Parental protein coverage: 81.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDALVEDDICILNHEKAHRRDPVTPVSIYAGDESVASHFALVTAYEDIKKRLKDSEKENSLLKKRIRFLE
          MDAL..DDICILN.EKAH.RDPVTPVSIY.GDESV.S.FALV.AYEDIKKRLK.SEKENS.LKKR.RFLE
Retrocopy MDALIDDDICILNQEKAHERDPVTPVSIYSGDESVTSRFALVIAYEDIKKRLKESEKENSFLKKRVRFLE

Parental  EKLIGARFDEETSSVGREQVNKAYHAYREVCIDRDNLKNK-LDKMNKDNSESLKVLNEQLQSKEVELLQL
          EKLIGA..DEET.SVGREQ.NKAYHAY.EV.IDR..LKN..L.KMN..N.E.LK.LNEQ.QSKEV..LQL
Retrocopy EKLIGAQLDEETYSVGREQLNKAYHAY*EVYIDREILKNN>LNKMNQNNPEPLKALNEQVQSKEVKRLQL

Parental  RTEVETQQVMRNLNSPSSNWEVEKLNCDLKIHGLEKELELMRKECSNLKIELQKAKQTDPSEDDNLKNCT
          RTEV.TQ.VMRN.N.P..NWE.EKLNCDL.IHGLEKELEL.RKECS.LKIELQKAKQ.DPSE.DNLKN..
Retrocopy RTEVGTQ*VMRNSNPPLRNWELEKLNCDLMIHGLEKELELVRKECSDLKIELQKAKQMDPSEEDNLKNSA

Parental  LQRVSISSDNMQH-AYWELKREMSNLHLVTQVQAELLRKLKTPTTIKKAYTPAACTEDLGKDSTKLHLTN
          L.R.SIS.DNMQ...YWELKREMS.LHL.TQVQAE.LRKLK.PT..KKA..P..C.EDLGK...K..L..
Retrocopy LRRASISRDNMQQ<VYWELKREMSDLHLMTQVQAERLRKLKMPTAFKKACAPLTCAEDLGKEH-KTPLDK

Parental  F-TASYKRHAPLSPNGKAV-CHTTSSPFPGDTKILSEKEVLQ
          F.TASYKRH..LSPNGKAV..HTTSSP.PGD.KILS.K...Q
Retrocopy F>TASYKRHVCLSPNGKAV<FHTTSSPLPGDIKILSKKKKKQ

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	30.80 RPM
SRP017611_kidney	0.20 RPM	22.81 RPM
SRP017611_liver	0.15 RPM	9.48 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1778 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1778 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010432	2 retrocopies	retro_chof_1794, retro_chof_234,
Dasypus novemcinctus	ENSDNOG00000011053	2 retrocopies	retro_dnov_1377, retro_dnov_542,
Homo sapiens	ENSG00000163512	2 retrocopies	retro_hsap_1491, retro_hsap_1564,
Gorilla gorilla	ENSGGOG00000022881	2 retrocopies	retro_ggor_1145, retro_ggor_1189,
Loxodonta africana	ENSLAFG00000008538	2 retrocopies	retro_lafr_529, retro_lafr_925,
Myotis lucifugus	ENSMLUG00000000043	3 retrocopies	retro_mluc_1707, retro_mluc_435, retro_mluc_611,
Macaca mulatta	ENSMMUG00000000056	1 retrocopy	retro_mmul_2135,
Monodelphis domestica	ENSMODG00000015075	1 retrocopy	retro_mdom_1786,
Nomascus leucogenys	ENSNLEG00000004069	1 retrocopy	retro_nleu_1714,
Oryctolagus cuniculus	ENSOCUG00000014956	1 retrocopy	retro_ocun_1778 ,
Otolemur garnettii	ENSOGAG00000005896	1 retrocopy	retro_ogar_3078,
Pongo abelii	ENSPPYG00000014053	2 retrocopies	retro_pabe_1241, retro_pabe_3784,
Pan troglodytes	ENSPTRG00000014707	1 retrocopy	retro_ptro_1052,
Tursiops truncatus	ENSTTRG00000016434	1 retrocopy	retro_ttru_1093,