RetrogeneDB ID: retro_rnor_2046

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:31874060..31874690(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1564865
• Ensembl ID: ENSRNOG00000038361
• Aliases: RGD1564865, RGD1309566
• Description: 20-alpha-hydroxysteroid dehydrogenase-like [Source:RefSeq peptide;Acc:NP_001157868]

Sequence

>retro_rnor_2046
TATCTTATTCATAACTTGATATTAATTAAGTCATCAGAGGAGATATATGCAAAAGATGAGAATGGAAAAGTATTGTTTGA
GATAGTAGATCTCTGTGCTATGAGGGAGGCATTGGAGATATATAAGGATGCAGGATTGGCCAAGTCCATCAGGATGTCCA
ACTTTAATCACGGGAAGCTGGAGATGGTCCTGAACAAGTCAGAGCTCAATTACAAGCCTGTGTGGGACCAGGTAGAATGT
CACCGTTATCTGAACCAGAGCCAGCTACTGGAGTTCTGCAAGTCAAGAGACATTATTCTGGTTGTCTACCAGGCCCTGGG
GTCTCAGCATCCTATAACTTGGGTGGACAAGAATGCCCCATTTCTTTTGAATAGTCCAGTTCTTTGTGCCATGGCCAAAA
AGCACAATCAAAGTCCAACTCAGATTGCCCTTCGCTACCAGGTACAGCATGGGGTTGTTGCCCTGGCCCATAGTTATGAA
GAGAATGAGATGCAAGAGAACATTTGAGTATTTGAATTCCAGTCGCCTTTAGAGAATCTGGCAGTCCGAGATGGCCTGAA
CAGACGCTTCAGATCTTTTCCTGTGGACATTGCTGCTGGACACCCCAGTTTTCCATTTTTTAATGGATAT

Alignment

ORF - retro_rnor_2046 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.52 %
• Parental protein coverage: 71.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YLIHYPISIKPSEEIYTKDENGKILFETVDLCAIWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLK
          YLIH..I.IK.SEEIY.KDENGK.LFE.VDLCA..EA.E..KDAGLAKSI..SNFN...LEM.LNK..L.
Retrocopy YLIHNLILIKSSEEIYAKDENGKVLFEIVDLCAMREALEIYKDAGLAKSIRMSNFNHGKLEMVLNKSELN

Parental  HRPVCNQVECHPYLNQSKLMDFCKSQDIVLVAYAALGSQRPTNWVDKNAPFLLNDPVLGGMAKKHNRSPA
          ..PV..QVECH.YLNQS.L..FCKS.DI.LV.Y.ALGSQ.P..WVDKNAPFLLN.PVL..MAKKHN.SP.
Retrocopy YKPVWDQVECHRYLNQSQLLEFCKSRDIILVVYQALGSQHPITWVDKNAPFLLNSPVLCAMAKKHNQSPT

Parental  QIALRYQVQRGVVALAQTYEQKEMKENIQVFEFQLPSEDMEVLDGLNRNFRYFPVNIAAEHPNYPYSDDY
          QIALRYQVQ.GVVALA..YE..EM.ENI.VFEFQ.P.E...V.DGLNR.FR.FPV.IAA.HP..P....Y
Retrocopy QIALRYQVQHGVVALAHSYEENEMQENI*VFEFQSPLENLAVRDGLNRRFRSFPVDIAAGHPSFPFFNGY

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	0.00 RPM
SRP017611_kidney	0.00 RPM	116.05 RPM
SRP017611_liver	0.00 RPM	1.28 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2046 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2046 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2046 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008668	1 retrocopy	retro_chof_568,
Echinops telfairi	ENSETEG00000009155	1 retrocopy	retro_etel_352,
Rattus norvegicus	ENSRNOG00000009513	1 retrocopy	retro_rnor_1438,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Rattus norvegicus	ENSRNOG00000013004	1 retrocopy	retro_rnor_2559,
Rattus norvegicus	ENSRNOG00000017165	1 retrocopy	retro_rnor_1441,
Rattus norvegicus	ENSRNOG00000038361	1 retrocopy	retro_rnor_2046 ,
Sarcophilus harrisii	ENSSHAG00000006005	1 retrocopy	retro_shar_520,