RetrogeneDB ID: retro_ocun_1273

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 5:30851445..30852350(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHA3
• Ensembl ID: ENSOCUG00000005495
• Aliases: None
• Description: pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3 [Source:HGNC Symbol;Acc:14338]

Sequence

>retro_ocun_1273
ATGGAGGGGGTTCTGTACAAGTGGACCAATATCTCACGAATTGGCAGCCTCGCTAGTTTGTTTTAGATAATGGAATCCTA
TCCTACTATGATTCACAAGATGATGTTTGCAAAGGGAGCAAAGGAAGTATAAAGATGGCGTTTGTGAAATTAAAGTCCAT
TCAGCAGACAACACGAGAACGGAATTAATCATTCCAGGAGAGCCGCATCTCTACAAGAAAGCGGTAAATGCAGCTGAAAG
ACGGACAGAAGTGGCTGGTTGCTCTCAGGAGCTCCAACGGGTGTTCGACTGATACTAGGATTAAAAAAGAAAAAGAAAGA
AGTGAAACTAGTGAATCTCTGGAAACCAAAATATCTGAAGCTCGCCTGCACCGTGACCTCCAAATGCAGACGTTCATGCA
ATCAGGAACGAGTCCGCCATGATGAGAATCATTCATCTCCCAGCACAGAGAATATGCATGAAGCTGCTTCTCTGCTCAGT
GCTACATGGAAACATTCATCATGACCCTTGAGGAATGTGCGAAGAGAGCAAATGCCAAGTTTAAGCCTGCGATGTTTCAA
CTGCCCCATCAGGATCTTTGAGTTTCTCCCGTGTCACCTTCTCCTGTTCCAAAGATGATGTTCTGTGCCCACCCACCCAG
GTTCTCGTAGTTCAGAAAGGCATAGCCACCGGATGAAAGAGCCAGCATCTGCACTTTACTTACTCTCCCAGTGATGCCAA
GGAACCTGCTCAGATACAGACTCATGGAGTGAGATTCCCCTTGAAGAACGGATACACCTGCTCACTGTGACAGAAATACA
CTTAATGGAAACTTGACATCAGCAACCATTCCTGACGAAAACAGACTTAAGGGAAAAAAAAAAAAAAAGCCTGAATTGGA
AGATCCTCTTCCATCCTCTTCCTCA

Alignment

ORF - retro_ocun_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MEGVLYKWTN-YLTGWQPRWFVLDNGILSYYDSQDDVCKGSKGSIKMA-VCEIKVHSADNTRMELIIPGE
          MEGVLYKWTN.YLT.WQPR.FVLDNGILSYYDSQDDVCKGSKGSIKMA.VCEIKVHSADNTR.ELIIPGE
Retrocopy MEGVLYKWTN<YLTNWQPR*FVLDNGILSYYDSQDDVCKGSKGSIKMA<VCEIKVHSADNTRTELIIPGE

Parental  QHFYMKAVN-AAER-QRWLVALGSSKACLTDTRTKKEKEISETSESLKTKMSELRLYCDLLMQ-QVHTI-
          .H.Y.KAVN.A..R.Q.WLVAL.SS..C.TDTR.KKEKE.SETSESL.TK.SE.RL..DL.MQ..VH.I.
Retrocopy PHLYKKAVNAAERR>QKWLVALRSSNGCSTDTRIKKEKERSETSESLETKISEARLHRDLQMQ<DVHAI<

Parental  QEFVHHDESRSSPSIENMNEASSLLSAT-CNTFITTLEECVKIANAKFKPEMFQLPHPDPLVSPVSPSPV
          QE.V.HDE..SSPS.ENM.EA.SLLSAT...TFI.TLEEC.K.ANAKFKP.MFQLPH.D..VSPVSPSPV
Retrocopy QERVRHDENHSSPSTENMHEAASLLSAT<METFIMTLEECAKRANAKFKPAMFQLPHQDL*VSPVSPSPV

Parental  QMMKRSV-SHPGSCNSERSSHCTKEPVSTLHRLSQRRRRTYSDTDSCNDIPLEE-SDRPTHCSRNTLNGD
          ..M......HPGS..SER.SH..KEP.S.L..LSQ....T.SDTDS...IPLEE..D.P.HC.RNTLNG.
Retrocopy PKMMFCA>THPGSRSSERHSHRMKEPASALYLLSQ*CQGTCSDTDSWSEIPLEE<TDTPAHCDRNTLNGN

Parental  LTSATIPEENRLTA--KKKPESEALLPPFSS
          LTSATIP.ENRL....KKKPE.E..LP..SS
Retrocopy LTSATIPDENRLKGKKKKKPELEDPLPSSSS

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	0.17 RPM	19.10 RPM
SRP017611_kidney	0.00 RPM	16.72 RPM
SRP017611_liver	0.00 RPM	4.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1273 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1273 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013997	5 retrocopies	retro_chof_1366, retro_chof_1559, retro_chof_300, retro_chof_736, retro_chof_985,
Cavia porcellus	ENSCPOG00000003906	1 retrocopy	retro_cpor_487,
Dasypus novemcinctus	ENSDNOG00000002717	1 retrocopy	retro_dnov_107,
Erinaceus europaeus	ENSEEUG00000004169	1 retrocopy	retro_eeur_416,
Homo sapiens	ENSG00000116095	1 retrocopy	retro_hsap_2060,
Macropus eugenii	ENSMEUG00000015317	2 retrocopies	retro_meug_1530, retro_meug_341,
Microcebus murinus	ENSMICG00000009898	1 retrocopy	retro_mmur_617,
Myotis lucifugus	ENSMLUG00000005823	2 retrocopies	retro_mluc_1031, retro_mluc_689,
Oryctolagus cuniculus	ENSOCUG00000005495	1 retrocopy	retro_ocun_1273 ,
Otolemur garnettii	ENSOGAG00000002724	1 retrocopy	retro_ogar_1845,
Tupaia belangeri	ENSTBEG00000007550	3 retrocopies	retro_tbel_4186, retro_tbel_4555, retro_tbel_4723,
Tarsius syrichta	ENSTSYG00000005341	1 retrocopy	retro_tsyr_869,
Tursiops truncatus	ENSTTRG00000009729	2 retrocopies	retro_ttru_1296, retro_ttru_1497,
Vicugna pacos	ENSVPAG00000003490	3 retrocopies	retro_vpac_487, retro_vpac_578, retro_vpac_619,