RetrogeneDB ID: retro_ocun_322

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:164075624..164076312(+)
• Located in intron of: ENSOCUG00000026462

Retrocopy information

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

Parental gene information

• Parental gene symbol: DLST
• Ensembl ID: ENSOCUG00000015606
• Aliases: None
• Description: dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex) [Source:HGNC Symbol;Acc:2911]

Sequence

>retro_ocun_322
GAAGATCAGGAGAAAATAAACAAGATGTGACAGTGCATTGTTCAGCATCTAAAGGAAACTTAGAATACATGTGCAATACT
GATGACTTTCAATGAGATTGATTTGAGTAACATTCAATATATGAAAGCTTAGCACAAGGATGCTTTTCTGAAGAAACATA
CCTCAAACTAGGGTTTATGTTGTCATTTGCGAAGCCCTTAGCATTTGCCTCGCAGGAGCAGCCTGTGGTAAATGCACTGA
TTGAGGAGTCAGCCAAGGAGATGGTATACAGGATTACATTGACATCAGTGTTGTATTGGCGATTCCACAGGTTCTGTTGG
TTCTGTCATCAGGAATATGAAAGCTATTATTAATGCTGAAATTGAATGAGCCGTCGGTGAACTTGGAGAGATGTAAAAGA
ATGAACTTGCCTTTGAAGGCATGGATGGCTGTACTTTCTTCATTAGCACTGGAAGTATTTTTGGCTTGTTCTTTAGAACA
CCTTTATCAAGCTCCCCCAGTCTGCCATCAGGTTCTGCATGTCATTTTTAACAGGGCAGTGACAATGGGAGACAATGTGG
AAGTGTGGACCATGATGTATGAGGCTTTGACTTTCAGTCACCGGATGATTGATAGCAAAGAGAACAATACTTTATTCTGA
CAAATCAAGTCATCAGTAGAGCATCCCAGAGTCCTTTCCTTAAGCATT

Alignment

ORF - retro_ocun_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.23 %
• Parental protein coverage: 51.56 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EHREKMNRMRQRIAQRLKEAQNTCAMLTTFNEIDMSNIQEMRARHKDAFLKKHN-LKLGFMSAFVKASAF
          E..EK.N.M.Q.I.Q.LKE..NTCA.L.TFNEID.SNIQ.M.A.HKDAFLKKH..LKLGFM..F.K..AF
Retrocopy EDQEKINKM*QCIVQHLKET*NTCAILMTFNEIDLSNIQYMKA*HKDAFLKKHT<LKLGFMLSFAKPLAF

Parental  ALQEQPIVNAVIDDSTKEVVYR-DYIDISVAVATPRGLVV-PVIRNVETMNYADIERTISELGEKARKNE
          A.QEQP.VNA.I..S.KE.VYR.DYIDISV..A.P..L.V..VIRN......A.IE....ELGE...KNE
Retrocopy ASQEQPVVNALIEESAKEMVYR<DYIDISVVLAIPQVLLV<SVIRNMKAIINAEIE*AVGELGE-M*KNE

Parental  LAIEDMDGGTFTISNGGVFGSLFGTPI-INPPQSAI-LGMHAIFDRPVAVGGKVEVRPMMFVALTYDHRL
          LA.E.MDG.TF.IS.G..FG..F.TP..I..PQSAI....H.IF.R.V..G..VEV..MM..ALT..HR.
Retrocopy LAFEGMDGCTFFISTGSIFGLFFRTPL<IKLPQSAI<QVLHVIFNRAVTMGDNVEVWTMMYEALTFSHRM

Parental  IDGREAVTFLRKIKAAVEDPRVLLLDL
          ID..E..T....IK..VE.PRVL.L..
Retrocopy IDSKENNTLF*QIKSSVEHPRVLSLSI

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	0.06 RPM	74.89 RPM
SRP017611_kidney	0.00 RPM	172.41 RPM
SRP017611_liver	0.00 RPM	36.53 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_322 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_322 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
Cavia porcellus	ENSCPOG00000009316	1 retrocopy	retro_cpor_1089,
Homo sapiens	ENSG00000119689	1 retrocopy	retro_hsap_407,
Gorilla gorilla	ENSGGOG00000011591	1 retrocopy	retro_ggor_403,
Nomascus leucogenys	ENSNLEG00000016330	1 retrocopy	retro_nleu_1006,
Oryctolagus cuniculus	ENSOCUG00000015606	1 retrocopy	retro_ocun_322 ,
Pan troglodytes	ENSPTRG00000006543	1 retrocopy	retro_ptro_312,
Tursiops truncatus	ENSTTRG00000001915	1 retrocopy	retro_ttru_681,
Xenopus tropicalis	ENSXETG00000013264	1 retrocopy	retro_xtro_46,