RetrogeneDB ID: retro_ocun_952

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:64210924..64212191(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DBT
• Ensembl ID: ENSOCUG00000014244
• Aliases: None
• Description: dihydrolipoamide branched chain transacylase E2 [Source:HGNC Symbol;Acc:2698]

Sequence

>retro_ocun_952
GCTCTACATGGACAGATTGTTCAGTTCAAACTCTCAGACATTGGAGAAGGGATTAGAGAAGTAACTGTTAAAGAATGGTA
TGTAAAAGAAGGAGATACAGTGTCTCAGTTTGATAGCATCTGTGAAGTCCAGAGTGATAAAGCTTCTGTTACCATCACTA
GTCGTTATGATGGAGTCATTAAAAAGCTCTATTATAATCTAGATGATATTGCCTATGTGGGGAAGCCATTAGTAGACATA
GAAACAGAAGCTTTAAAAGATTCAGAAGAAGATGTTGAAACTCCAGCTGTGTCTCATGATGAACACACACACCAAGAAAT
AAAGGGTCAAAAAACACTGGCTACTCCTGCAGTTCGCCGTCTTGCAATGGAAAACAACATTAAGCTAAGTGAAGTTGTTG
GCTCAGGAAAAGATGGCAGAATACTTAAAGAAGATATTCTCAACTACTTGGAAAAGCAAACAGGAGCTATATTGCCTCCT
TCACCAAAAGCTGAAGTTATGCCACCTCCACCAAAACCATAGGACAAGACTATTCCCATGCCAATATCAAAACCTCCAGT
ATTCATAGGCAAAGACAAAACAGAACCCATAAAAGGCTTTCAAAAAGCAATGGTCAAGAGTATGTCTGCAGCTCTAAAGA
TACCTCACTTTGGTTATTGTGATGAGGTTGACCTTACTGAACTGGTTAAGCTACGAGAAGAATTGAAACCCATTGCTTTG
GCTCGTGGAATTAAGCTTTCCTTTATGCCCTTCTTCTTAAAGGCAGCTTCCTTGGGATTGCTAGTTTCCTATCCTTAATG
ATTCTGTGGATGAAGGCTGCCAGAATATAACATATAAGGCTTCTCATAATATTGGGATAGCAATGGATACTGAGCAGGGA
TTGATTGTCCCCAATGTCAAAAACGTTCAGATCTGCTCTGTATTTGAGATCGCCACTGAGCTGAACCGCCTCCAGAAACT
GGGCACCGCAGGTCAGCTCAGCACCACAGATCTTACCGGAGGAACATTCACTCTTTCCAATATTGGATCCATTGGTGGTA
CCTATGCCAAACCTGTGATATTGCCACCTGAAGTAGCCATTGGGGCCCTTGGATCAATTAAGGCCCTTCCTCAATTTAAC
CAGAAAGGAGAAGTATATCCTGCGCAGATAATGAATGTGAGCTGGTCAGCTGATCACAGAATTATTGATGGTGCTACAAT
GTCAAGCTTCTCTAATTTGTGGAAATCCTACTTAGAAAACCCATCTTTTATGCTACTGGATTTGAAA

Alignment

ORF - retro_ocun_952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.42 %
• Parental protein coverage: 87.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALHGQIVQFKLSDIGEGIREVTVKEWYVKEGDTVSQFDSICEVQSDKASVTITSRYDGVIKKLYYNLDDI
          ALHGQIVQFKLSDIGEGIREVTVKEWYVKEGDTVSQFDSICEVQSDKASVTITSRYDGVIKKLYYNLDDI
Retrocopy ALHGQIVQFKLSDIGEGIREVTVKEWYVKEGDTVSQFDSICEVQSDKASVTITSRYDGVIKKLYYNLDDI

Parental  AYVGKPLVDIETEALKDSEEDVVETPAVSHDEHTHQEIKGQKTLATPAVRRLAMENNIKLSEVVGSGKDG
          AYVGKPLVDIETEALKDSEEDV.ETPAVSHDEHTHQEIKGQKTLATPAVRRLAMENNIKLSEVVGSGKDG
Retrocopy AYVGKPLVDIETEALKDSEEDV-ETPAVSHDEHTHQEIKGQKTLATPAVRRLAMENNIKLSEVVGSGKDG

Parental  RILKEDILNYLEKQTGAILPPSPKAEVMPPPPKPKDKTIPMPISKPPVFIGKDKTEPIKGFQKAMVKTMS
          RILKEDILNYLEKQTGAILPPSPKAEVMPPPPKP.DKTIPMPISKPPVFIGKDKTEPIKGFQKAMVK.MS
Retrocopy RILKEDILNYLEKQTGAILPPSPKAEVMPPPPKP*DKTIPMPISKPPVFIGKDKTEPIKGFQKAMVKSMS

Parental  AALKIPHFGYCDEVDLTELVKLREELKPIALARGIKLSFMPFFLKAAS-LGLLQF-PILNASVDEGCQNI
          AALKIPHFGYCDEVDLTELVKLREELKPIALARGIKLSFMPFFLKAAS.LG...F.PILN.SVDEGCQNI
Retrocopy AALKIPHFGYCDEVDLTELVKLREELKPIALARGIKLSFMPFFLKAAS<LGIASF<PILNDSVDEGCQNI

Parental  TYKASHNIGIAMDTEQGLIVPNVKNVQICSVFEIATELNRLQKLGTAGQLSTTDLTGGTFTLSNIGSIGG
          TYKASHNIGIAMDTEQGLIVPNVKNVQICSVFEIATELNRLQKLGTAGQLSTTDLTGGTFTLSNIGSIGG
Retrocopy TYKASHNIGIAMDTEQGLIVPNVKNVQICSVFEIATELNRLQKLGTAGQLSTTDLTGGTFTLSNIGSIGG

Parental  TYAKPVILPPEVAIGALGSIKALPRFNQKGEVYPAQIMNVSWSADHRIIDGATMSRFSNLWKSYLENPSF
          TYAKPVILPPEVAIGALGSIKALP.FNQKGEVYPAQIMNVSWSADHRIIDGATMS.FSNLWKSYLENPSF
Retrocopy TYAKPVILPPEVAIGALGSIKALPQFNQKGEVYPAQIMNVSWSADHRIIDGATMSSFSNLWKSYLENPSF

Parental  MLLDLK
          MLLDLK
Retrocopy MLLDLK

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	0.94 RPM	14.51 RPM
SRP017611_kidney	1.62 RPM	43.08 RPM
SRP017611_liver	1.16 RPM	17.26 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_952 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013258	2 retrocopies	retro_chof_52, retro_chof_655,
Microcebus murinus	ENSMICG00000006218	1 retrocopy	retro_mmur_1089,
Oryctolagus cuniculus	ENSOCUG00000014244	1 retrocopy	retro_ocun_952 ,
Otolemur garnettii	ENSOGAG00000005625	1 retrocopy	retro_ogar_2997,