RetrogeneDB ID: retro_rnor_219

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:166147861..166148779(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000024604
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Jkamp
• Ensembl ID: ENSRNOG00000004751
• Aliases: Jkamp, RGD1308917
• Description: JNK1/MAPK8-associated membrane protein [Source:RefSeq peptide;Acc:NP_001100208]

Sequence

>retro_rnor_219
ATGGCATGCTTTGGACTCTACTGTGGGAAGACCCTATTGTTTAAAAATAGCTCAACTGAAATATATGGAGAGTGCGGGGC
GTGTCCAAGAGGACAAAGAACAAATGAACAGAAGTACTGTCAGCCCTGCATGGAGTCCCCGGAACTTTATGACTGGCTTT
ACCTTGGCTTCATGGCGATGCTTCCTCTCGTTTCCCATTGGCTCTGCATTGAATGGGACGCAAAGGATAGTAATTCCAGA
GGTGCGTTTTTCCAGCAAGTCTCTGCATTATTAGAATGCAGCATGGCGGCTATAGTCACATTACTTGTGAGTGATCCGGT
CGGCACCCTTGCCATCCATTCGTGCCGGGTGCTGATGCTTTCAGATTGGTACACGATGCTCTACAATCCAAGCCCAGATT
ACATCACCACCGTGCACTGCACTCAGGAAGCCGTGTACCCGCTGTACACCATCGTGTTTGTGTATTATGCTTTCTGCTTA
GTGTTGATGCTGCTGCTTCGACCATTACTGGTGAAGAAGATCCAGTGGCACCTGTACATGCCAAACCAGCTGGAAAGCAT
TTACACTGCCCTCTACTTCTTCCCGGTTTTGACGGTGCTGCAAGCAGTTGCCGGAGGCCTCTTATATTATGCCTTCCCAT
ACATTGTATTGGTGACATCTTTGGCTAATCTGGCTGTATATCTGGTTTTTGTCAAAATAGAGAGCTACAGTGATCTGATG
AAAAAGGACAGACTTCTTGTCCTCTTCAGCCACTGGTTTCTTCACGCCTATGGCTTAATCGCACTCTCCAGAGGGCAGCA
ACTTGAACAAGATCTGCTCCTTTTAACTTTGGTGCCTTTCCCCACTCTTTTTTACTTTTTCACTACCAAATTTACCAAAC
CGTCACGGATAATCTCTGAAGGAACCAAAGGACACTGA

Alignment

ORF - retro_rnor_219 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.1 %
• Parental protein coverage: 97.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ACLGLYCGKTLLFKNGSSEIYGECGVCPRGQRTNAQKYCQPCTESPELYDWLYLGFMAMLPLVLHWFFIE
          AC.GLYCGKTLLFKN.S.EIYGECG.CPRGQRTN.QKYCQPC.ESPELYDWLYLGFMAMLPLV.HW..IE
Retrocopy ACFGLYCGKTLLFKNSSTEIYGECGACPRGQRTNEQKYCQPCMESPELYDWLYLGFMAMLPLVSHWLCIE

Parental  WYSGKKSS-SALFQHITALFECTMAAIITLLVSDPVGVLYIRSCRVLMLSDWYTMLYNPSPDYVTTVHCT
          W......S..A.FQ...AL.EC.MAAI.TLLVSDPVG.L.I.SCRVLMLSDWYTMLYNPSPDY.TTVHCT
Retrocopy WDAKDSNSRGAFFQQVSALLECSMAAIVTLLVSDPVGTLAIHSCRVLMLSDWYTMLYNPSPDYITTVHCT

Parental  HEAVYPLYTIVFVYYAFCLVLMMLLRPLLVKKIACGLGKSDRFKSIYAALYFFPILTVLQAVGGGLLYYA
          .EAVYPLYTIVFVYYAFCLVLM.LLRPLLVKKI...L.......SIY.ALYFFP.LTVLQAV.GGLLYYA
Retrocopy QEAVYPLYTIVFVYYAFCLVLMLLLRPLLVKKIQWHLYMPNQLESIYTALYFFPVLTVLQAVAGGLLYYA

Parental  FPYIILVLSLVTLAVYMSASEIENCYDLLVRKKRLIVLFSHWLLHAYGIVSISRVDRLEHDLPLLALVPT
          FPYI.LV.SL..LAVY.....IE..Y..L..K.RL.VLFSHW.LHAYG....SR...LE.DL.LL.LVP.
Retrocopy FPYIVLVTSLANLAVYLVFVKIES-YSDLMKKDRLLVLFSHWFLHAYGLIALSRGQQLEQDLLLLTLVPF

Parental  PALFYLFTAKFTEPSRILSEGANGH
          P.LFY.FT.KFT.PSRI.SEG..GH
Retrocopy PTLFYFFTTKFTKPSRIISEGTKGH

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	31.63 RPM
SRP017611_kidney	0.00 RPM	26.66 RPM
SRP017611_liver	0.00 RPM	11.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_219 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_219 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_104

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000050130	1 retrocopy	retro_hsap_4132,
Macaca mulatta	ENSMMUG00000008715	1 retrocopy	retro_mmul_1188,
Mus musculus	ENSMUSG00000005078	1 retrocopy	retro_mmus_104,
Pan troglodytes	ENSPTRG00000006400	1 retrocopy	retro_ptro_2808,
Rattus norvegicus	ENSRNOG00000004751	1 retrocopy	retro_rnor_219 ,
Tupaia belangeri	ENSTBEG00000002820	1 retrocopy	retro_tbel_2109,