RetrogeneDB ID: retro_ocun_1338

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:172044974..172045811(+)
• Located in intron of: ENSOCUG00000002211

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005941
• Aliases: None
• Description: None

Sequence

>retro_ocun_1338
GCTACCCACTTGCTTGCAGGAGCCAGGGCAAGGAGCGGGCCACTGGGCACTGTGGCCCTGAACCACACGGAAGAGTGCAC
CGGCCCCACGCGGAGGACTGCCACCTCTTTTTCAAGAATGCATCTGCTCACTACATTTCCCCCTTTCGTGGTATTCCTCT
GATAGTGGACTCTAAGGAGGAAAATGGCATTCCTACAAAGCAAGCACGAAATGATTAATATGAGAGTTTGTTTAACATGG
TTGTAGAAGCACCTCGGTGGACAAATGCTAAAATGGAGATTGCCACCGAGGAGCCTTTGAATCCCATTAAGCGAGATGTT
CAGCACAGCAAGCCGCACTCTGTGGCAACTCTCTTCCCTCACAAGGGTTGTCTGTGGATTATGTGCCCGCCCGCCTGCAG
ACTCGGGAGATCCCCAACAAGCAGATGAGCACACACTGCCGTGCAGATAACGATCCTCTTGATGTCTGTGAAATCGGCCC
TGAGGTTCTGACTGGTAGAGAGGTCGCTCATGTGAAGATTCTTGGAATTTTGGCTCTGATTGATGAGGGGGAAACGGATT
GGAAATTAACTGCTACCAGTACTAATGATCCTGAAGCCTCAAAGGTTGATGACACTGCTGATGTTAGAAGTTCAAACCTG
GTTACCTGGAAGCTACTCTTACCTGGTTTAAGTTTTAGAAAGCACCAGATGGAAAACCAGAAAACCAGTTTGCTTTTAAT
AAAGAATTCAGAAACAAGGCTTTTGCTCTTGCGGTTATTAAATCTATTCATGATCACCGGACAGCACTGCTCATGAAGAG
AAGCAGTGGAGGGACAATAAGTTGCACAAACGTGCAG

Alignment

ORF - retro_ocun_1338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.13 %
• Parental protein coverage: 82.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAHPPAGARARSGPLRAMALYHTEERG-RPHSEDYRLFFKNVAGHYISPFHDIPLKVESKEENGIPTKKA
          A.H..AGARARSGPL...AL.HTEE...RPH.ED..LFFKN...HYISPF..IPL.V.SKEENGIPTK.A
Retrocopy ATHLLAGARARSGPLGTVALNHTEECT<RPHAEDCHLFFKNASAHYISPFRGIPLIVDSKEENGIPTKQA

Parental  RNDEYENLFNMVVEVPRWTNAKMEIATKEPLNPIKQDVKHGKLRYVANIF-PHKGYIWNY-GALPQTWED
          RND.YE.LFNMVVE.PRWTNAKMEIAT.EPLNPIK.DV.H.K...VA..F.P..G....Y..A..QT.E.
Retrocopy RND*YESLFNMVVEAPRWTNAKMEIATEEPLNPIKRDVQHSKPHSVATLF<PSQGLSVDYVPARLQTREI

Parental  PHQTDESTNCCGDNDPIDVCEIGSKVLTRGEVVHVKILGILALIDEGETDWKLIAINANDPEASKFDDID
          P.....ST.C..DNDP.DVCEIG..VLT..EV.HVKILGILALIDEGETDWKL.A...NDPEASK.DD..
Retrocopy PNK-QMSTHCRADNDPLDVCEIGPEVLTGREVAHVKILGILALIDEGETDWKLTATSTNDPEASKVDDTA

Parental  DVK-KFKPGYLEATLNWFKFYKVPDGKPENQFAFNGEFRNKAFALEVIKSTHDHWKALLMKKCDGGAINC
          DV..KFKPGYLEATL.WFKF.K.PDGKPENQFAFN.EFRNKAFAL.VIKS.HDH..ALLMK...GG.I.C
Retrocopy DVR<KFKPGYLEATLTWFKF*KAPDGKPENQFAFNKEFRNKAFALAVIKSIHDHRTALLMKRSSGGTISC

Parental  TNVQ
          TNVQ
Retrocopy TNVQ

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	19.48 RPM
SRP017611_kidney	0.00 RPM	50.68 RPM
SRP017611_liver	0.00 RPM	4.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1338 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1338 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010887	1 retrocopy	retro_cfam_405,
Choloepus hoffmanni	ENSCHOG00000008731	3 retrocopies	retro_chof_1052, retro_chof_430, retro_chof_769,
Echinops telfairi	ENSETEG00000014816	1 retrocopy	retro_etel_1959,
Macaca mulatta	ENSMMUG00000017004	1 retrocopy	retro_mmul_1278,
Monodelphis domestica	ENSMODG00000020635	5 retrocopies	retro_mdom_638, retro_mdom_795, retro_mdom_945, retro_mdom_946, retro_mdom_947,
Oryctolagus cuniculus	ENSOCUG00000005941	2 retrocopies	retro_ocun_1338 , retro_ocun_1470,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Ochotona princeps	ENSOPRG00000007086	1 retrocopy	retro_opri_847,
Sus scrofa	ENSSSCG00000022365	1 retrocopy	retro_sscr_557,
Tursiops truncatus	ENSTTRG00000003141	2 retrocopies	retro_ttru_1307, retro_ttru_606,