RetrogeneDB ID: retro_ocun_497

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:23186841..23187571(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FECH
• Ensembl ID: ENSOCUG00000003020
• Aliases: None
• Description: ferrochelatase [Source:HGNC Symbol;Acc:3647]

Sequence

>retro_ocun_497
GGCCCTGAAACCCTCACAGAAGTTCACCACTTCCTTCTGAGGCTCTTCTTGGACTGAGAGCCCAGGACATTTCCAAAGTG
GACTGGCAGTATTGTGTCCAAATGCCAAATTTCCAAAATTCAAGCACAGTGCCACAGGAGTGAAGGTGGGTCCCCCCTCA
GGATGTGGGTTTCCAAACAAGGAGAAGGCAGGGTGAAGCTCCTTGATGAGTTGGTCCCCATATAGCCTCTCACACATTTT
TATTGGATACTGGAAATGTCCATGCTTTAATTGAAGAAGAAATTGAAGAAATGAAGAAAGAGGGACAAGAAAGGGCTGTT
GTTTTCACACAGTACCCCAGTACTGTTGTTCTACCATGAGCAGCAGCTTAAATGGAATTTACAGATACTGTAGTGGAGCA
GGAAAGAAGCCTGCCATGAGGTGGAGCACTGCTGACTGTGGCCCACACATCCTGTCCTCATCCAGTGTTTTCCAGACCTC
ATTCTGAAAGTACTGGACCATTTTCCACTTAAGAAGAAAGGGAGGTGAATATTCTGTTCTCTGCTCACTTTCTGCCAATG
TCAGTGTTCAACAGAAGGGACCCCTATCCTCAAGAGGTAGGTGCAACCATCCACAGAGTCATGGAAAGGCTGTGTTACTC
CAACCCCTACCAGCTGCTTCTGCAGCACAACGTTGGTCTAATTCCTGGTTTTATCCTCAAACAGATAAGGTCATCAAAGG
GCTTTGTGAA

Alignment

ORF - retro_ocun_497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.1 %
• Parental protein coverage: 58.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GPETLGEVHDFLLRLFLDRDLMTLPVQSKLGPFIAKRRTSKIQEQYRRIGGGSPIKMWTSKQGEGMVKLL
          GPETL.EVH.FLLRLFLD....T.P.....G....K...SKIQ.Q..R..GGSP..MW.SKQGEG.VKLL
Retrocopy GPETLTEVHHFLLRLFLD*EPRTFPKWT--GSIVSKCQISKIQAQCHRSEGGSPLRMWVSKQGEGRVKLL

Parental  DEL-SPHTAPHKYYIGFRYVHPLTEEAIEEMERDGLERAIAFTQYP-QYSCSTTGSSLNAIYRYYNGAGK
          DEL..PH.A.H........VH.L.E.........G.ERA..FTQYP.QY.CST..SSLN.IYRY..GAGK
Retrocopy DEL<GPHIASHTFLLDTGNVHALIEXXXXXXXXEGQERAVVFTQYP<QYCCSTMSSSLNGIYRYCSGAGK

Parental  KPAMRWSTID-RWPTHPLLIQCFADHILKELDRFPPEKRS-EVVILFSAHSLPMSVVNRGDPYPQEVGAT
          KPAMRWST.D..WPTHP.LIQCF.D.ILK.LD.FP..K...EV.ILFSAH.LPMSV.NR.DPYPQEVGAT
Retrocopy KPAMRWSTAD<LWPTHPVLIQCFPDLILKVLDHFPLKKKG<EVNILFSAHFLPMSVFNRRDPYPQEVGAT

Parental  VHRVMERLGYSNPYRLVWQSKVGPMP-WLGPQTDETIRGLCE
          .HRVMERL.YSNPY.L..Q..VG..P.W..PQTD..I.GLCE
Retrocopy IHRVMERLCYSNPYQLLLQHNVGLIP<WFYPQTDKVIKGLCE

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	13.47 RPM
SRP017611_kidney	0.00 RPM	11.86 RPM
SRP017611_liver	0.00 RPM	9.02 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_497 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_497 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_497 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003873	1 retrocopy	retro_cjac_4008,
Homo sapiens	ENSG00000066926	1 retrocopy	retro_hsap_2631,
Gorilla gorilla	ENSGGOG00000005554	1 retrocopy	retro_ggor_1841,
Macaca mulatta	ENSMMUG00000022568	1 retrocopy	retro_mmul_1485,
Nomascus leucogenys	ENSNLEG00000008062	1 retrocopy	retro_nleu_643,
Oryctolagus cuniculus	ENSOCUG00000003020	1 retrocopy	retro_ocun_497 ,
Pongo abelii	ENSPPYG00000009182	1 retrocopy	retro_pabe_2332,
Pan troglodytes	ENSPTRG00000010045	1 retrocopy	retro_ptro_1776,