RetrogeneDB ID: retro_rnor_1874

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:29284550..29285289(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Wbp1
• Ensembl ID: ENSRNOG00000008720
• Aliases: None
• Description: WW domain-binding protein 1 [Source:RefSeq peptide;Acc:NP_001100070]

Sequence

>retro_rnor_1874
CTTCAGGTGCTGCAACAGCTTCTTCAAGAGCTGTGCCCAGGAGTTAATACCTAGCCTACATCTGTGAGAGTGGTCATTGC
TATGTGGAGACTGGTTGCTGTACCTACTACTGTGAACTCTGGGAGTTCTGGCTGCTTTGGACTGTCCTCATCCTCTTGAG
TTGTTGTGCCTCCCGCCACTGAAGAGCTAAACTTAGGCTGCAGCAGCAGCAGTGGCAGCGTGAAATCAACTTGTTTACCA
TGGAGCATGTTATGGGACTGGCCCTGTTCCAATTGGTTCACTGCTTGACCTTCACCTCTTCTGAGCCTTCAAACCCCCAG
CCTATGAGGATGTGGTTTAGTACCCAGGAACACTGACACCTCCTTAAACTATGGCCCCTGGTTACCCATTACTTCTAAGG
AATGTACCAGCTAGTCTTCCGAATCCAGCTGCCCTGCCCACTTGGAAGGGACAAATGTAGGTTTTTCCTCCCACCAGAGT
GCTCTCCCTCATTAGGTGAGCCCCAGGGCAGGATGGAGCCCAGTCCACATAAGCCCTTCCTGCCACTATTGTTGTCTGAT
TGATGGCTCAGGTATTGAGCTCTGACCTTGTCTTGACTCCAGCGAAGGTGAGCCAGTCAAGGAGGTAAGGGCTAGTGCCA
CCCAACCAGATCTGGAGTACCATTCCCCCTTGTGCACTGCCTCCAGATTTTATGTCCCAGGCCCTTCCCTTGGGCCTGGT
TTCTAGTTATGGGAACATC

Alignment

ORF - retro_rnor_1874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.31 %
• Parental protein coverage: 93.68 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LQAPQQQLRELCPGVNTQP-YLCESGHCCGETGCCTYYYELWWFWLLWTVLILFSCCCAFRHRRAKLRLQ
          LQ..QQ.L.ELCPGVNT.P.Y.CESGHC..ETGCCTYY.ELW.FWLLWTVLIL.SCC.A.RH.RAKLRL.
Retrocopy LQVLQQLLQELCPGVNT*P<YICESGHCYVETGCCTYYCELWEFWLLWTVLILLSCC-ASRH*RAKLRL-

Parental  QQQRQREI-NLLAYHGACHGAGPVPTGSLLDLRLLSAFKPPAYEDVVHHPGTPPPPYTMAPGH-PLTTSN
          QQQ......N.L.YHGAC.G.GPVP.GSLLDL.L..AFKPPAYEDVV..PGT..PP.TMAPG..P.T.S.
Retrocopy QQQQWQRE<NQLVYHGACYGTGPVPIGSLLDLHLF*AFKPPAYEDVV*YPGTLTPP*TMAPGY<PIT-SK

Parental  ECTRCSSESSCSAQSEGTSVEGVSSNQSALPPQEGEPRAGVSPVHTPPSCRYRHLTGDSGIELCPCPDSS
          ECT..SSESSC.A..EGT.V.G.SS.QSALP.....PRAG.SPVH..PSC.Y..L...SGIEL.PC.DSS
Retrocopy ECTS*SSESSCPAHLEGTNV-GFSSHQSALP-H*VSPRAGWSPVHISPSCHYCCLIDGSGIEL*PCLDSS

Parental  EGELVKELRASATQPDLEDHS-PCALPPEPMSQVPPVGLASSYGDI
          EGE.VKE.RASATQPDLE.HS.PCALPP..MSQ..P.GL.SSYG.I
Retrocopy EGEPVKEVRASATQPDLEYHS>PCALPPDFMSQALPLGLVSSYGNI

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	25.95 RPM
SRP017611_kidney	0.00 RPM	42.99 RPM
SRP017611_liver	0.00 RPM	21.11 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1874 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1874 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1874 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000239779	2 retrocopies	retro_hsap_2125, retro_hsap_2290,
Rattus norvegicus	ENSRNOG00000008720	1 retrocopy	retro_rnor_1874 ,