RetrogeneDB ID: retro_rnor_2763

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: JH620491.1:2..788(+)
• Located in intron of: None

Retrocopy information

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

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_2763
TGGCGTATGGGCGGGCTGCTGAGAAGACGCTTCCCAACCTGCTTGTCTCCTTGGAAGATTCCTCCTCGTGTCCTCAAATC
CTCACAACCGGAAGCTCTAGTCAGTCTGACAAACAATGCAGTAGCCTTTGCACCTCTGCAGACACTTACTGATGAGGAAA
TTATGATGAAGCAGACAGTCAAAAAATTTGCACAGGAGCACGTTGCTCCTCTGGTTTCCTCTATGGATGAGAACTCAAAA
ATGGAGAAATCGGTGATCCAGGGATTGTTCCAGCAAGGGCTGATGGGCATTGAAGTTGAAGCACAATATGGAGGGACAGA
AGCTTCCTTTTTCTGCTCTGTCCTAGTGATAGAGGAACTAGCTAAGGTGGATGCTTCGGTGGCTCTCCTGTGTGACATCC
AGAACACAATAATTAACAACCTGTTTAGAAAACACGCTTCAGAAGAACAGAAGGCCACCTATTTGCCAAAGCTGGTTACA
GAAAAATTAGGGAGCTTTTGCCCCTCTGAAGCTGGAGCCGGTAGCGACTCTTTCGCTATGAAAACAAGAGCTGATAAAAG
TGGAAATTACTACGTCCTCAATGGGTCGAAGATGTGGATCAGCCATGCCGAGCATGCAGAGCTCTTCCTGGTCTTCGCCA
ATGTGGACCCCAGCTCTGGCTACAGAGGCATCACCTGCTTCTTAGTAGACCGAGATACAGAAGGTTTCCAGATAGGGAAA
CGAGAAAATAAAATGGGCATCAGAGCTTCATCCACCTGTCAGTTAACATTTGAAAATGTTAAGGTT

Alignment

ORF - retro_rnor_2763 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.17 %
• Parental protein coverage: 69.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WRAGGLLRRNFLTHSSSWKIPPRVLKSSQPEALLSVTNNALCFAPLQTFTDEDIMMQKAVKKFAQEQIAP
          WR.GGLLRR.F.T..S.WKIPPRVLKSSQPEAL.S.TNNA..FAPLQT.TDE.IMM...VKKFAQE..AP
Retrocopy WRMGGLLRRRFPTCLSPWKIPPRVLKSSQPEALVSLTNNAVAFAPLQTLTDEEIMMKQTVKKFAQEHVAP

Parental  LVSTMDENSKMEKSVIQGLFQQGMMGIEVEAKYGGTEASFLCSVLVIEELAKVDASVALLCDIQNTVINK
          LVS.MDENSKMEKSVIQGLFQQG.MGIEVEA.YGGTEASF.CSVLVIEELAKVDASVALLCDIQNT.IN.
Retrocopy LVSSMDENSKMEKSVIQGLFQQGLMGIEVEAQYGGTEASFFCSVLVIEELAKVDASVALLCDIQNTIINN

Parental  LFRKHGTEEQKATYLPKLVTEKLGSFCLSEAGAGSDSFALKTRADKSGNYYVINGSKMWISNAEHAELFL
          LFRKH..EEQKATYLPKLVTEKLGSFC.SEAGAGSDSFA.KTRADKSGNYYV.NGSKMWIS.AEHAELFL
Retrocopy LFRKHASEEQKATYLPKLVTEKLGSFCPSEAGAGSDSFAMKTRADKSGNYYVLNGSKMWISHAEHAELFL

Parental  VFANVDPPSGYRGITCFLVDRDTEGFQIGRRENKMGIRASSTCQLTFENVKV
          VFANVDP.SGYRGITCFLVDRDTEGFQIG.RENKMGIRASSTCQLTFENVKV
Retrocopy VFANVDPSSGYRGITCFLVDRDTEGFQIGKRENKMGIRASSTCQLTFENVKV

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	0.00 RPM	51.43 RPM
SRP017611_liver	0.00 RPM	48.68 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2763 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2763 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2763 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,