RetrogeneDB ID: retro_ocun_1604

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018711:87186..87688(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL7L1
• Ensembl ID: ENSOCUG00000003844
• Aliases: None
• Description: ribosomal protein L7-like 1 [Source:HGNC Symbol;Acc:21370]

Sequence

>retro_ocun_1604
CCTTGGAAGAGCCTGGCAGACTTTGATTTATATATCCAAAGGATTAACGGGGTGAGTTCACTTGAGGAGAGGGCCATTAC
AAGACTTCACCAGGAGCAAATGTTCAGTGACTTTTGTCAAAGTCACCCCACCCCCACAAAATCTGAAAATATTGCATGTG
GTGGAAGATTAAGTAACCTAGAAATTTCCAAATCCGAAGTCTGCCTGGGAACTGTATCTTGAAACATGGTGAGTTGAAAC
AAGCTTAGGTAACTATTAAGACGAGACCTCCGACAAGCAACACAATTATTGAGTACCTGGGGGAAATTTGTTGTAATTTG
TGTGAAGACCTCACTCATGGGGTTGCCTTCTGGGAAAGCATATTGAGGGGATCTCAGGGTTCCTGTGCCCTTTCCAACTG
ATGGCCACTCGTATTTGCAAGAATCCCGTGGCCTTCCTCAAGGAGATGGTCTCACCTGGCGATCACAGTGAATGAATCAG
TCAGCTCATCTACCAGCTAAAC

Alignment

ORF - retro_ocun_1604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.29 %
• Parental protein coverage: 66.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PDKHSLAFVVRLQRINGVSSLVERTIARLRLKKLFSGVFVQ-VTP--QNLKLLRIVEPYVTWGFPNLKSV
          P.K....F....QRINGVSSL.ER.I.RL.....FS..F.Q.VTP..QNLK.L..VE..VT..FPN.KS.
Retrocopy PWKSLADFDLYIQRINGVSSLEERAITRLHQEQMFSD-FCQ>VTPPPQNLKILHVVED*VT*KFPNPKSA

Parental  REL-ILKRG---QARVNDKSIPLTDNTVIEEHLG-RFGVICL-EDLIHEIAF-PGKYFQNIARFLRPFQL
          .EL.ILK.G...QA.V..K..P.T.NT.I.E.LG..F.VIC..EDL.H..AF..GK....I..FL.PFQL
Retrocopy WEL>ILKHGELKQA*VTIKTRPPTSNTII-EYLG>KFVVICV<EDLTHGVAF<LGKHIEGISGFLCPFQL

Parental  SVARHASKNRVGFLKEMGSPGYRGERINQLIRQLN
          ..A....KN.V.FLKEM.SPG...E.I.QLI.QLN
Retrocopy -MATRICKNPVAFLKEMVSPGDHSE*ISQLIYQLN

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	0.00 RPM	14.18 RPM
SRP017611_kidney	0.10 RPM	20.47 RPM
SRP017611_liver	0.00 RPM	11.79 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1604 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1604 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 84 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012791	2 retrocopies	retro_amel_1260, retro_amel_243,
Bos taurus	ENSBTAG00000018478	2 retrocopies	retro_btau_588, retro_btau_816,
Canis familiaris	ENSCAFG00000001728	4 retrocopies	retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Choloepus hoffmanni	ENSCHOG00000000306	4 retrocopies	retro_chof_1168, retro_chof_1404, retro_chof_388, retro_chof_478,
Cavia porcellus	ENSCPOG00000021189	2 retrocopies	retro_cpor_1134, retro_cpor_653,
Dasypus novemcinctus	ENSDNOG00000013485	1 retrocopy	retro_dnov_689,
Equus caballus	ENSECAG00000003113	1 retrocopy	retro_ecab_998,
Erinaceus europaeus	ENSEEUG00000010431	1 retrocopy	retro_eeur_90,
Echinops telfairi	ENSETEG00000002419	3 retrocopies	retro_etel_1151, retro_etel_1823, retro_etel_542,
Felis catus	ENSFCAG00000009707	1 retrocopy	retro_fcat_143,
Gorilla gorilla	ENSGGOG00000009958	15 retrocopies	retro_ggor_1009, retro_ggor_1013, retro_ggor_1253, retro_ggor_1261, retro_ggor_1904, retro_ggor_2099, retro_ggor_2108, retro_ggor_2113, retro_ggor_2162, retro_ggor_2282, retro_ggor_2457, retro_ggor_2524, retro_ggor_2591, retro_ggor_2659, retro_ggor_2973,
Macaca mulatta	ENSMMUG00000021313	1 retrocopy	retro_mmul_11,
Monodelphis domestica	ENSMODG00000019028	1 retrocopy	retro_mdom_1708,
Mustela putorius furo	ENSMPUG00000013296	1 retrocopy	retro_mputfur_1577,
Mus musculus	ENSMUSG00000063888	4 retrocopies	retro_mmus_2359, retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Oryctolagus cuniculus	ENSOCUG00000003844	6 retrocopies	retro_ocun_1393, retro_ocun_1604 , retro_ocun_1818, retro_ocun_278, retro_ocun_509, retro_ocun_598,
Oryctolagus cuniculus	ENSOCUG00000008407	12 retrocopies	retro_ocun_109, retro_ocun_1164, retro_ocun_1282, retro_ocun_1342, retro_ocun_1494, retro_ocun_1646, retro_ocun_1879, retro_ocun_456, retro_ocun_501, retro_ocun_718, retro_ocun_727, retro_ocun_785,
Otolemur garnettii	ENSOGAG00000012671	3 retrocopies	retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
Pteropus vampyrus	ENSPVAG00000008696	3 retrocopies	retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Rattus norvegicus	ENSRNOG00000016269	1 retrocopy	retro_rnor_2795,
Sorex araneus	ENSSARG00000005286	2 retrocopies	retro_sara_100, retro_sara_211,
Sarcophilus harrisii	ENSSHAG00000011219	1 retrocopy	retro_shar_216,
Sus scrofa	ENSSSCG00000026472	3 retrocopies	retro_sscr_198, retro_sscr_756, retro_sscr_807,
Ictidomys tridecemlineatus	ENSSTOG00000009841	2 retrocopies	retro_itri_1233, retro_itri_417,
Tursiops truncatus	ENSTTRG00000006971	6 retrocopies	retro_ttru_1194, retro_ttru_171, retro_ttru_361, retro_ttru_498, retro_ttru_528, retro_ttru_915,
Vicugna pacos	ENSVPAG00000008894	2 retrocopies	retro_vpac_386, retro_vpac_584,