RetrogeneDB ID: retro_rnor_2753

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: AABR06111084.1:17..1157(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046278
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Acadsb
• Ensembl ID: ENSRNOG00000020624
• Aliases: None
• Description: Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P70584]

Sequence

>retro_rnor_2753
ATGGCGGTCTCTGCCCTTAGCTGTGGCGTATGGGCGGGCTGCTGAGAAGACGCTTCCCAACCTGCTTGTCTCCTTGGAAG
ATTCCTCCTCGTGTCCTCAAATCCTCACAACCGGAAGCTCTAGTCAGTCTGACAAACAATGCAGTAGCCTTTGCACCTCT
GCAGACACTTACTGATGAGGAAATTATGATGAAGCAGACAGTCAAAAAATTTGCACAGGAGCACGTTGCTCCTCTGGTTT
CCTCTATGGATGAGAACTCAAAAATGGAGAAATCGGTGATCCAGGGATTGTTCCAGCAAGGGCTGATGGGCATTGAAGTT
GAAGCACAATATGGAGGGACAGAAGCTTCCTTTTTCTGCTCTGTCCTAGTGATAGAGGAACTAGCTAAGGTGGATGCTTC
GGTGGCTCTCCTGTGTGACATCCAGAACACAATAATTAACAACCTGTTTAGAAAACACGCTTCAGAAGAACAGAAGGCCA
CCTATTTGCCAAAGCTGGTTACAGAAAAATTAGGGAGCTTTTGCCCCTCTGAAGCTGGAGCCGGTAGCGACTCTTTCGCT
ATGAAAACAAGAGCTGATAAAAGTGGAAATTACTACGTCCTCAATGGGTCGAAGATGTGGATCAGCCATGCCGAGCATGC
AGAGCTCTTCCTGGTCTTCGCCAATGTGGACCCCAGCTCTGGCTACAGAGGCATCACCTGCTTCTTAGTAGACCGAGATA
CAGAAGGTTTCCAGATAGGGAAACGAGAAAATAAAATGGGCATCAGAGCTTCATCCACCTGTCAGTTAACATTTGAAAAT
GTTAAGGTTCCAGAGACTAATATTTTGGGGAAAATTGGGCATGGTTATAAGTATGCCATAGGAAGTCTTAATGAAAGGGT
AGAAATCGGAATTGCTGCACAGAAATGCTAGGGACTGGCCCCAAGGGATGTTTTGACTACCTATTCCATACATTAAAGAA
AGGATGCAGTTTTTGGCAAAACGAATATTTGATTTTCAGGGGCTCCAACACCCCTTTAATGAGGTGGCCACCCAGCTGGA
AGCCACACGGTTGGTAANATANAANGNTGNTAGGNTNGTAGAAGNNGTCAGGCCATTTATAAAAGAAGCATCTATGGCCA
AATATTATGCATCTGAGGTC

Alignment

ORF - retro_rnor_2753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVSAFQ-LWRAGGLLRRNFLTHSSSWKIPPRVLKSSQPEALLSVTNNALCFAPLQTFTDEDIMMQKAVK
          MAVSA...LWR.GGLLRR.F.T..S.WKIPPRVLKSSQPEAL.S.TNNA..FAPLQT.TDE.IMM...VK
Retrocopy MAVSALS<LWRMGGLLRRRFPTCLSPWKIPPRVLKSSQPEALVSLTNNAVAFAPLQTLTDEEIMMKQTVK

Parental  KFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGMMGIEVEAKYGGTEASFLCSVLVIEELAKVDASVALLC
          KFAQE..APLVS.MDENSKMEKSVIQGLFQQG.MGIEVEA.YGGTEASF.CSVLVIEELAKVDASVALLC
Retrocopy KFAQEHVAPLVSSMDENSKMEKSVIQGLFQQGLMGIEVEAQYGGTEASFFCSVLVIEELAKVDASVALLC

Parental  DIQNTVINKLFRKHGTEEQKATYLPKLVTEKLGSFCLSEAGAGSDSFALKTRADKSGNYYVINGSKMWIS
          DIQNT.IN.LFRKH..EEQKATYLPKLVTEKLGSFC.SEAGAGSDSFA.KTRADKSGNYYV.NGSKMWIS
Retrocopy DIQNTIINNLFRKHASEEQKATYLPKLVTEKLGSFCPSEAGAGSDSFAMKTRADKSGNYYVLNGSKMWIS

Parental  NAEHAELFLVFANVDPPSGYRGITCFLVDRDTEGFQIGRRENKMGIRASSTCQLTFENVKVPETSVLGKI
          .AEHAELFLVFANVDP.SGYRGITCFLVDRDTEGFQIG.RENKMGIRASSTCQLTFENVKVPET..LGKI
Retrocopy HAEHAELFLVFANVDPSSGYRGITCFLVDRDTEGFQIGKRENKMGIRASSTCQLTFENVKVPETNILGKI

Parental  GHGYKYAIGSLNEG-RIGIAAQML-GLA-QGCFDYTIPYIKERMQF-GKRIFDFQGLQHQVAHVATQLEA
          GHGYKYAIGSLNE...IGIAAQ...GLA.QG.F...IPYIKERMQF..KRIFDFQGLQH....VATQLEA
Retrocopy GHGYKYAIGSLNERVEIGIAAQKC*GLA>QGMF*LPIPYIKERMQFLAKRIFDFQGLQHPFNEVATQLEA

Parental  ARLLTYNAARLVEAGRPFIKEASMAKYYASEV
          .RL......R.VE..RPFIKEASMAKYYASEV
Retrocopy TRLVXXXXXRXVEXVRPFIKEASMAKYYASEV

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	17.90 RPM
SRP017611_kidney	0.91 RPM	51.43 RPM
SRP017611_liver	0.54 RPM	48.68 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2753 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2753 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2753 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017638	1 retrocopy	retro_ecab_8,
Rattus norvegicus	ENSRNOG00000020624	4 retrocopies	retro_rnor_2753 , retro_rnor_2762, retro_rnor_2763, retro_rnor_2764,