RetrogeneDB ID: retro_ocun_1884

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:37705208..37705869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT19
• Ensembl ID: ENSOCUG00000016132
• Aliases: None
• Description: keratin 19 [Source:HGNC Symbol;Acc:6436]

Sequence

>retro_ocun_1884
ATAGCTTTGAATAACGTCTGAACCAAGATTGAGATGGAGCAAGCCCTGCATTTGAGCATGAAGGCCGATATCACTGGCCT
GCGCTGGGTATTGGATGAACTGACTCTGCCTTGGACTGACTTGAAGATGCAGATTGAAGAGCTGAAGGAGGAGCTGACCT
TCCACAAAAGGAGCAACGGTGAGTAAATCACCGCCCTAAGGGGCCAGGTGGGTGCCCAGGTCAATGTGGAGATGGGTTCT
GCTTCAGATATTGACCTAATGAAGATCCTGAGTAAATGAGAATATAATATGAGGTCATGACTGAGAAGAACCAGAAGGAT
GCCAAAGCCTGGTTCACCAGCCAGCCAAAGGAGTTGAATTGAGAGGTGGCTGGCCACACAGAGCAATTCCAAATAAGCAG
GTCCAATGTCAGTTACCTGCCTTGTTCCCTCCAGAGTCTTAAGATGGAGCTGTAGTTGTAGCTCAGCATGAGAGCAAGCC
TATAAGGCACCCTGGCAGAGACAGAGGCCCACTTCATGGCATAGCTGGGGCAGATCTAGGCGCTGATCAGCAGTATGGAA
GCCCAGCTGAGGGATGGGCATATTAACCCTGAGTAGCAGAACCAGGAGTACCAGCAGCTCATGGACTTCAAGTGCTGCTG
AAGCAGGAGATTGCCACCTAC

Alignment

ORF - retro_ocun_1884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.54 %
• Parental protein coverage: 55.25 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LAADDFRTKFETEQALRLSVEADINGLRRVLDELTLARTDLELQIEGLKEELAYLKKNHEEEISALRGQV
          .A.....TK.E.EQAL.LS..ADI.GLR.VLDELTL..TDL..QIE.LKEEL...K....E.I.ALRGQV
Retrocopy IALNNV*TKIEMEQALHLSMKADITGLRWVLDELTLPWTDLKMQIEELKEELTFHKRSNGE*ITALRGQV

Parental  GGQVSVEVDSAPGIDLGKILSE-MRSQYEVMAEKNRKDAEAWFNSRTEELSREVAVNTEQLKSSRSEVTD
          G.QV.VE..SA..IDL.KILS..MR..YEVM.EKN.KDA.AWF.S...EL..EVA..TEQ...SRS.V..
Retrocopy GAQVNVEMGSASDIDLMKILSK<MRI*YEVMTEKNQKDAKAWFTSQPKELN*EVAGHTEQFQISRSNVSY

Parental  LRRTMQGLEIELQSQLSMKAALEGTLAETEARYGAQLAQIQAVISSIEAQLSDVRADTERQNQEYQQLMD
          L....Q.L..EL...LSM.A.L.GTLAETEA...A.L.QI.A.ISS.EAQL.D.....E.QNQEYQQLMD
Retrocopy LPCSLQSLKMEL*L*LSMRASL*GTLAETEAHFMA*LGQI*ALISSMEAQLRDGHINPE*QNQEYQQLMD

Parental  IKS-RLEQEIATY
          .K...L.QEIATY
Retrocopy FKC<LLKQEIATY

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	0.22 RPM
SRP017611_kidney	0.00 RPM	52.10 RPM
SRP017611_liver	0.00 RPM	4.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1884 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1884 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1884 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884 ,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337, retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697,