RetrogeneDB ID: retro_rnor_1441

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:10625142..10625721(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Akr1e2
• Ensembl ID: ENSRNOG00000017165
• Aliases: Akr1e2, Akr1cl2, Akr1e1
• Description: 1,5-anhydro-D-fructose reductase [Source:UniProtKB/Swiss-Prot;Acc:Q5U1Y4]

Sequence

>retro_rnor_1441
GGCTTCAAGCCTGGGTCTGAGTATCTCCCACTGGATGTATCAGGAAACGTGGTTCCTAGTGACACCAATGTTGTGGACAC
TTGGACGGACAACTATGGAACAACTAGTGGATGGAGGTTTGGTAAAAGCAATTGGTGTCTCCAACTTCACCCCTCTTCAG
ATTGAGGGGATCTTGAACAAACCTGGCTTAAAGTATAAGCCTGCCATTAACCAGATCGAGTGCCACCCATACCTAACTCA
GGAGAAGCTGATCGAGTACTGCCATTGTAAAGGCATCGCGGTGACTGCATACAGTCCCCTTGGTTCTCCTAAAGACCTTT
CTCTCCTGGAGAATCCCAGGATCAAGGACATTGCAGCCAAGTACAATAAAACTGCAGCCCAGGTGCTGATCCAGTTCCTC
ATTCAAAGGAACTTGGTAGTGATCCCCAACTCTGTGACACCAGCACGAATTGCTGAGAACTTTAAGGCCTTTGACTTTGA
GCCGAGCAGCAAGGACATGACACTCTACTCAGCTACAACAGGAGGGTGTGTGCCTTGGTGAGCTGTGCCAAACACAAGGG
TTACCCCTTCCACTCAGAA

Alignment

ORF - retro_rnor_1441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.53 %
• Parental protein coverage: 64.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GFKPGDKDIPLDRSGKVIPSHTSFLDTW-EAMEDLVIEG-LVKNIGVSNFNHEQLDRLLNKPGLRIKPIT
          GFKPG....PLD.SG.V.PS.T...DTW..........G.LVK.IGVSNF...Q....LNKPGL..KP..
Retrocopy GFKPGSEYLPLDVSGNVVPSDTNVVDTW>RTTMEQLVDGGLVKAIGVSNFTPLQIEGILNKPGLKYKPAI

Parental  NQIECHPYLNQKSLIDFCHGRNVSVTAYRPLGGSRDGVHLMDDIVIRKIAKKHGKSPAQILIRFQIQRNL
          NQIECHPYL.Q..LI..CH.....VTAY.PLG...D...L.....I..IA.K..K..AQ.LI.F.IQRNL
Retrocopy NQIECHPYLTQEKLIEYCHCKGIAVTAYSPLGSPKD-LSLLENPRIKDIAAKYNKTAAQVLIQFLIQRNL

Parental  IVIPKSVNPSRIRENIQVFDFELTEKDM-EELLSLDKNLRLATFPSTENHKDYPFHIE
          .VIP.SV.P.RI.EN...FDFE...KDM...LLS...N.R.....S...HK.YPFH.E
Retrocopy VVIPNSVTPARIAENFKAFDFEPSSKDM<DTLLSY--NRRVCALVSCAKHKGYPFHSE

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	12.15 RPM
SRP017611_kidney	0.00 RPM	47.59 RPM
SRP017611_liver	0.00 RPM	52.38 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1441 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1441 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000018481	1 retrocopy	retro_mdom_1687,
Mustela putorius furo	ENSMPUG00000016247	1 retrocopy	retro_mputfur_65,
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,