RetrogeneDB ID: retro_rnor_1713

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:5149989..5150665(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam108c1
• Ensembl ID: ENSRNOG00000012683
• Aliases: Abhd17c, Fam108c1, RGD1308210
• Description: abhydrolase domain-containing protein FAM108C1 [Source:RefSeq peptide;Acc:NP_001094206]

Sequence

>retro_rnor_1713
CAGTACTCGCAGCACGAACTGGACGCATTAGAGATCTTCTTCTCGCGCATGTCCCCTGACAACCGTGTGGGCTGCAAGTT
CCTGCGCTGGGCGCTCTCCAGACAGCCGCTCTTCTCACACCGCAACGCAGTGGACTTGGCCCAGACCTGTAGCTTCTACA
TCCGCATGGGCTCGCGAATCAACTGCAATATCTTCTCTTACGACTATTGAGCCTATGGGGTGAACTCCAGGCAAGCCCTC
TAAAAAGAATCTCTAAGCTGAAATCAACGCTGCATGCCAGGCGCTGTGCACCCGGTATGGCCTGAGTCCTGAGAATATTA
TCCTCTATGGACAGAGCATTGGCACCCTCCCCACTCTGGACCTGGCCTCGCGGTATGAGTGTGCAGCCATCATCCTCCAT
TCCCCTCTGCTGTCTGGATTGCGTGTTGCTTTTCCGGATGCCAGGAAAACATACTGCTTTGATGTTTCCTCCAGCATGGC
AAGATATCTAAAGTCTCCTGTGTTGATCATTCATGGTACAGTCATCGATTTCTCCCAATGCTTGGTGATATGTGAGCGCT
GTCCCCGTGCTGTTGAGCCCCTGTGGGTTGAGGGGGCTGGGCACAATGATTTAGAGCTCTAAGTACAGTACCTACAACGA
CTAAAACAGTTCATATCTCCGGAGCTTCCCAATTCC

Alignment

ORF - retro_rnor_1713 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.82 %
• Parental protein coverage: 72.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QYSQRELDAVEVFFSRTARDNRLGCMFVRCAPSSRYTLLFSHGNAVDLGQMCSFYIGLGSRINCNIFSYD
          QYSQ.ELDA.E.FFSR...DNR.GC.F.R.A.S.....LFSH.NAVDL.Q.CSFYI..GSRINCNIFSYD
Retrocopy QYSQHELDALEIFFSRMSPDNRVGCKFLRWALSRQP--LFSHRNAVDLAQTCSFYIRMGSRINCNIFSYD

Parental  YSGYGVSS-GKPSEKNLYADIDAAWQALRTRYGVSPENIILYGQSIGTVPTVDLASRYECAAVILHSPLM
          Y..YGV.S.GKPS.KNL.A.I.AA.QAL.TRYG.SPENIILYGQSIGT.PT.DLASRYECAA.ILHSPL.
Retrocopy Y*AYGVNS>GKPSKKNL*AEINAACQALCTRYGLSPENIILYGQSIGTLPTLDLASRYECAAIILHSPLL

Parental  SGLRVAFPDTRKTYCFDAFPSIDKISKVTSPVLVIHGTEDEVIDFSHGLAMYERCPRAVEPLWVEGAGHN
          SGLRVAFPD.RKTYCFD...S.....K..SPVL.IHGT...VIDFS..L...ERCPRAVEPLWVEGAGHN
Retrocopy SGLRVAFPDARKTYCFDVSSSMARYLK--SPVLIIHGT---VIDFSQCLVICERCPRAVEPLWVEGAGHN

Parental  DIELYAQYLERLKQFISHELPNS
          D.EL..QYL.RLKQFIS.ELPNS
Retrocopy DLEL*VQYLQRLKQFISPELPNS

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	18.84 RPM
SRP017611_kidney	0.00 RPM	154.64 RPM
SRP017611_liver	0.00 RPM	31.47 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1713 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1713 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1713 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000012683	2 retrocopies	retro_rnor_1713 , retro_rnor_1714,
Tarsius syrichta	ENSTSYG00000009403	3 retrocopies	retro_tsyr_1518, retro_tsyr_1994, retro_tsyr_2110,
Tursiops truncatus	ENSTTRG00000005787	1 retrocopy	retro_ttru_1580,