RetrogeneDB ID: retro_ocun_1560

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018700:9185476..9186139(+)
• Located in intron of: None

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_1560
ATTGTAGGCATTGGCTTGGTAGCCAGAGAGACTGTGTTGGATGTGCTACCACATTTTGATAAAGATTATGAAGTGCCTGG
TGTGTGGGAAGCGGCTGCAGCCCTGGTGGAGGAGTTAACTAGCTGATACTGACTCACTAAAAACTACCTGAACTATCTGA
CAGCCCTGGATTATTGTAATTTTGAAACAGACATACTGAGAAATGAGTTTGAAAGATAGGCTTCTCGTCAACCCATTGAA
CTACTCAGTATGAAACAATATGAACTTCCAGCACCATCCTCTGACATTAATGTGTGGCAAGGATGTGTAAACATTCTATG
GAGCAGTTAAGAGCACCACAAAATTCAAATTGAGAATCTGGAAATGATGTCACAGCATGGATGCAATTCCTGGGAAGTAT
ATAATAAAAGTCTAAGTCACATGATTGAACATGGCCAAAAAGAGGCTCAGAAGTTAAGGAAGCACATTCAAACTTTAAAC
TCGCAGTGAAAGAATATGCAGCTCAGAGCTGGATATAAATTGAGAGAAATGGAGTCAAACTGGGTATTCCTGGTCAGTAA
GGACTATGAGTTTGGATGGGCTACTGTGTAAGCAGAAAATGAAATATATCAAATTAAGCAGTAACATGGAGAAGCCAGTA
AAGAAAATATCTTTCAACACTTC

Alignment

ORF - retro_ocun_1560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGTGLVAGEVVVDALPYFDQGYEAPGVREAAAALVEEETRRYRPTKNYLSYLTAPDYSAFETDIMRNEF
          ..G.GLVA.E.V.D.LP.FD..YE.PGV.EAAAALVEE.T..Y..TKNYL.YLTA.DY..FETDI.RNEF
Retrocopy IVGIGLVARETVLDVLPHFDKDYEVPGVWEAAAALVEELTS*Y*LTKNYLNYLTALDYCNFETDILRNEF

Parental  ERLAARQPIELLSMKRYELPAPSSGQKNDITAWQECVNNSMAQLEHQAVRIENLELMSQHGCNAWKVYNE
          ER.A.RQPIELLSMK.YELPAPSS....DI..WQ.CVN......EH....IENLE.MSQHGCN.W.VYN.
Retrocopy ER*ASRQPIELLSMKQYELPAPSS----DINVWQGCVNILWSS*EHHKIQIENLEMMSQHGCNSWEVYNK

Parental  NLVHMIEHAQKELQKLRKHIQDLNWQRKNMQLTAGSKLREMESNWVSLVSKNYEIERTIVQLENEIYQIK
          .L.HMIEH.QKE.QKLRKHIQ.LN.Q.KNMQL.AG.KLREMESNWV.LVSK.YE.....V..ENEIYQIK
Retrocopy SLSHMIEHGQKEAQKLRKHIQTLNSQ*KNMQLRAGYKLREMESNWVFLVSKDYEFGWATV*AENEIYQIK

Parental  QQHGEANKENIRQDF
          Q.HGEA.KENI.Q.F
Retrocopy Q*HGEASKENIFQHF

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	49.12 RPM
SRP017611_kidney	0.00 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_1560 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1560 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,