RetrogeneDB ID: retro_ocun_1443

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:30822715..30823151(-)
• Located in intron of: ENSOCUG00000009557

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCAS2
• Ensembl ID: ENSOCUG00000016784
• Aliases: None
• Description: breast carcinoma amplified sequence 2 [Source:HGNC Symbol;Acc:975]

Sequence

>retro_ocun_1443
CAAGGTGATAAAGCACCTGGTGGGCGAGAAGTGGCTGCAGCCCTGGTGAAGGAGGAAACTCCGGGATACCGACTCACTAA
AAATTAACTGAGCTACCTGACAGCCCGGGATTATTCTGCTTTGCAAACTGACATACTGAGAAATGAATTGGAAAGACTGG
CTGCTGGACAAACCAATTGCTCTGCTCAGTGTGAAACGATACGAGTTTTCCAGCCCCATTCTCAGGTCAGAAAATGACAT
TACTGCATGGCAAGAATGTGTAAACAATTCTATGGCCCAGTTTAGAGCACCAAGTTGGAACTGAGAATCTGGAACTGATG
TCAGAGCACAGATGTGATGGCTGGAAAGTATGTAATGAAAATTTAGTTCCATGATTGAACATGCACAGAAAGAGCTTCAG
AAGTTAAGGAAACACATTCAAGCAAAAAACATGCAA

Alignment

ORF - retro_ocun_1443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.16 %
• Parental protein coverage: 64.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QGYEAPGVREAAAALVEEETRRYRPTKNYLSYLTAPDYSAFETDIMRNEFERLAARQ-PIELLSMKRYE-
          QG..APG.RE.AAALV.EET..YR.TKN.LSYLTA.DYSA..TDI.RNE.ERLAA.Q.PI.LLS.KRYE.
Retrocopy QGDKAPGGREVAAALVKEETPGYRLTKN*LSYLTARDYSALQTDILRNELERLAAGQ>PIALLSVKRYE>

Parental  LPAPSSGQK-NDITAWQECVNNSMAQ-LEHQAVRIENLELMSQHGCNAWKVYNENLV-HMIEHAQKELQK
          .PAP.SGQK.NDITAWQECVNNSMAQ.LEHQ.V..ENLELMS.H.C..WKV.NENLV..MIEHAQKELQK
Retrocopy FPAPFSGQK<NDITAWQECVNNSMAQ>LEHQ-VGTENLELMSEHRCDGWKVCNENLV<SMIEHAQKELQK

Parental  LRKHIQDLNWQ
          LRKHIQ..N.Q
Retrocopy LRKHIQAKNMQ

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	49.12 RPM
SRP017611_kidney	0.20 RPM	36.39 RPM
SRP017611_liver	0.00 RPM	15.65 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1443 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1443 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1443 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012448	1 retrocopy	retro_cjac_39,
Cavia porcellus	ENSCPOG00000020532	2 retrocopies	retro_cpor_1026, retro_cpor_1085,
Dasypus novemcinctus	ENSDNOG00000018484	2 retrocopies	retro_dnov_2350, retro_dnov_2617,
Homo sapiens	ENSG00000116752	2 retrocopies	retro_hsap_1220, retro_hsap_427,
Gorilla gorilla	ENSGGOG00000028233	2 retrocopies	retro_ggor_417, retro_ggor_949,
Loxodonta africana	ENSLAFG00000003183	1 retrocopy	retro_lafr_709,
Microcebus murinus	ENSMICG00000013720	1 retrocopy	retro_mmur_947,
Myotis lucifugus	ENSMLUG00000005653	3 retrocopies	retro_mluc_1018, retro_mluc_1609, retro_mluc_2307,
Macaca mulatta	ENSMMUG00000014496	1 retrocopy	retro_mmul_517,
Nomascus leucogenys	ENSNLEG00000004737	2 retrocopies	retro_nleu_1022, retro_nleu_692,
Oryctolagus cuniculus	ENSOCUG00000016784	2 retrocopies	retro_ocun_1443 , retro_ocun_1560,
Otolemur garnettii	ENSOGAG00000007544	3 retrocopies	retro_ogar_2847, retro_ogar_3226, retro_ogar_692,
Procavia capensis	ENSPCAG00000012077	1 retrocopy	retro_pcap_31,
Pongo abelii	ENSPPYG00000001000	2 retrocopies	retro_pabe_294, retro_pabe_716,
Pan troglodytes	ENSPTRG00000001136	3 retrocopies	retro_ptro_325, retro_ptro_557, retro_ptro_835,
Pteropus vampyrus	ENSPVAG00000008220	3 retrocopies	retro_pvam_1467, retro_pvam_285, retro_pvam_502,
Rattus norvegicus	ENSRNOG00000018783	1 retrocopy	retro_rnor_2864,
Sorex araneus	ENSSARG00000013847	2 retrocopies	retro_sara_144, retro_sara_180,
Sarcophilus harrisii	ENSSHAG00000008467	7 retrocopies	retro_shar_271, retro_shar_289, retro_shar_320, retro_shar_604, retro_shar_722, retro_shar_739, retro_shar_784,
Ictidomys tridecemlineatus	ENSSTOG00000014760	1 retrocopy	retro_itri_107,
Tupaia belangeri	ENSTBEG00000002231	1 retrocopy	retro_tbel_1418,
Taeniopygia guttata	ENSTGUG00000001012	1 retrocopy	retro_tgut_26,
Tarsius syrichta	ENSTSYG00000011964	2 retrocopies	retro_tsyr_1678, retro_tsyr_706,
Tursiops truncatus	ENSTTRG00000010759	1 retrocopy	retro_ttru_199,