RetrogeneDB ID: retro_ocun_1214

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:137002470..137003714(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFS1
• Ensembl ID: ENSOCUG00000017050
• Aliases: None
• Description: NFS1 nitrogen fixation 1 homolog (S. cerevisiae) (NFS1), nuclear gene encoding mitochondrial protein, mRNA [Source:RefSeq mRNA;Acc:NM_001171334]

Sequence

>retro_ocun_1214
CCTTCAGGCACAGCCGCTGCTCCGGAGGCACAGGCAGTGCTGCGACCTCTCTAGATGGATGCGCAAGCTACAACTCCTCT
GTACCCCCGGGTACTTGATGCCATGCTTCCTTATCTGGTCACCTACTATGGGAACCCACACTCCCGGACACACGCTTATG
GCTGGGAGAGTGAGGCAGCCGTGGAACACGCTCGCCAGCAAGTAGCATCTCTTATTGGAGCTGATCCTCGTGAGATCATT
TTCACTAGTGGTGCTACTGAATCCAACAACATAGCAATTAAGGGAGTGGCCAGGGTCTACAGGTCATGGAAAAAAACACT
TGATCACCACCCAGACAGAGCACAAATGTGTCTTGGACTCCTGCCATTCACCTGAAGCTGAGGGTTTTAAGGTCACCTAC
CTCCCCGTGCAGAAGAGTGGGATCATGACCTGCAGGAACTAGAGGCCGCCATCCAGCCAGATACCAGCCTGGTCTCCGTC
ATGACTGTGAACAATGAAATTGGAGTGAAGCGACTATTGCAGAGATAGGGAGGATTTGCAGTTTCAAAAAAAGTATATTT
TCATACCAATGCAGCCCAGACTGTTGGAAAAATCCCACTTGATGTCAACGACATGAAGATTGATCTCATGAGCATCAGTG
GTCACAAAATCTATGGTCCCAAAGGGGTTGGTGCCATCTACATCTGCCACCAGCCCCATGTGTGCGTGGAGGCCCTGCAG
AGTGGAGGTGGGCAGGAGCGGGGTCTAAGGTCTGGGACAGTGCCCACACCCCTGGTGGTGGGGATGGGGGCTGCGTGTGA
GGTGGCCCAGCAAGAGATTCAGTAGGACCATGAGTGGATTTCAAAGTTAGCAGAGCGGCTGACGCAGAAGATAATGAACA
GCCTTTCAGATGTGGTGATGAATGGAGACCCTGAGCAGCATTACCCTGGCTTATCAACCTTTCCTTTGCATACGTGGAAG
GGGAGAATTTGCTCATGGCACTTAAAGATGTCGCCTTATCTTCAGGGAGTGCCTGCACCTCTGTATCGCTGGAGCCCTCT
TACATCCTTAGAGCGATTGGCACTGATGAGGATTTAGCACACTCTTCTATCCGGTTTGGCATTGGCTGCTTCACTATGGA
GGAGGAAGTGGATTTCACGGTAGAGAAGTGTATTCATCACGTGAAGCGACTTCGAGAAATGAGCCCTCTCTGGGAGATGG
TGCAGGATGGCATTGACCTCAAGAGCATCAAGTGCACCCAACAC

Alignment

ORF - retro_ocun_1214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 90.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PSGTAAAPEVEAVLRPLYMDVQATTPLDPRVLDAMLPYLVNYYGNPHSRTHAYGWESEAAVERARQQVAS
          PSGTAAAPE..AVLRPL.MD.QATTPL.PRVLDAMLPYLV.YYGNPHSRTHAYGWESEAAVE.ARQQVAS
Retrocopy PSGTAAAPEAQAVLRPL*MDAQATTPLYPRVLDAMLPYLVTYYGNPHSRTHAYGWESEAAVEHARQQVAS

Parental  LIGADPREIIFTSGATESNNIAVKGVARFYRS-RKKHLITTQTEHKCVLDSCRSLEAEGFKVTYLPVQKS
          LIGADPREIIFTSGATESNNIA.KGVAR.YRS..KKHLITTQTEHKCVLDSC.S.EAEGFKVTYLPVQKS
Retrocopy LIGADPREIIFTSGATESNNIAIKGVARVYRS>GKKHLITTQTEHKCVLDSCHSPEAEGFKVTYLPVQKS

Parental  GII-DLQELEAAIQPDTSLVSVMTVNNEIGVKQ-PIAEIGRICS-SKKVYFHTDAAQAVGKIPLDVNDMK
          GI..DLQELEAAIQPDTSLVSVMTVNNEIGVK...IAEIGRICS.SKKVYFHT.AAQ.VGKIPLDVNDMK
Retrocopy GIM<DLQELEAAIQPDTSLVSVMTVNNEIGVKR<TIAEIGRICS>SKKVYFHTNAAQTVGKIPLDVNDMK

Parental  IDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGLRSGTVPTPLVVGMGAACEVAQQEMEYD
          IDLMSISGHKIYGPKGVGAIYI...P.V.VEALQSGGGQERGLRSGTVPTPLVVGMGAACEVAQQE...D
Retrocopy IDLMSISGHKIYGPKGVGAIYICHQPHVCVEALQSGGGQERGLRSGTVPTPLVVGMGAACEVAQQEIQ*D

Parental  HERISKLAERLTQKIMKSLPDVVMNGDPEQHYPGC-INLSFAYVEGESLLMALKDVALSSGSACTSASLE
          HE.ISKLAERLTQKIM.SL.DVVMNGDPEQHYPG..INLSFAYVEGE.LLMALKDVALSSGSACTS.SLE
Retrocopy HEWISKLAERLTQKIMNSLSDVVMNGDPEQHYPGL<INLSFAYVEGENLLMALKDVALSSGSACTSVSLE

Parental  PSYVLRAIGTDEDLAHSSIRFGIGRFTTEEEVDFTVEKCIHHVKRLREMSPLWEMVQDGIDLKSIKWTQH
          PSY.LRAIGTDEDLAHSSIRFGIG.FT.EEEVDFTVEKCIHHVKRLREMSPLWEMVQDGIDLKSIK.TQH
Retrocopy PSYILRAIGTDEDLAHSSIRFGIGCFTMEEEVDFTVEKCIHHVKRLREMSPLWEMVQDGIDLKSIKCTQH

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	19.87 RPM
SRP017611_kidney	0.00 RPM	98.72 RPM
SRP017611_liver	0.00 RPM	22.81 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1214 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1214 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1214 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000010393	1 retrocopy	retro_lafr_141,
Oryctolagus cuniculus	ENSOCUG00000002777	1 retrocopy	retro_ocun_405,
Oryctolagus cuniculus	ENSOCUG00000017050	1 retrocopy	retro_ocun_1214 ,
Tarsius syrichta	ENSTSYG00000005561	1 retrocopy	retro_tsyr_412,
Xenopus tropicalis	ENSXETG00000007430	1 retrocopy	retro_xtro_67,