RetrogeneDB ID: retro_rnor_2477

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:108397260..108397633(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000008326
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hypk
• Ensembl ID: ENSRNOG00000015703
• Aliases: Hypk, RGD1311457
• Description: Protein Hypk [Source:UniProtKB/TrEMBL;Acc:F1M8A5]

Sequence

>retro_rnor_2477
GAGATCGAAATGGCGACCGAGGGAGAAGTGAAACTGAAGTTAGAGTCTGAGATCAGCGGCCCTGAGCAGCCTCCTGCGAA
GCCAAGGAAACATGACAGTGGTGTTGCTGACCTAGAGCGGGTTACTGACTAAGCGGAGGAGGAAAGAGACCCAGAGTTTG
AATCTTGAGATGGCTATGTCCATCACTGGAGACAGACAGTCCAGGGAGCAAAAGGCCAAACAGGAGTGGGAGAAGGAACT
GGTGAAGATCACTATCAAGAAGGAAGATCTGGAGTTGATAATGACAGAAATGGAGATCTCTCGAGCAGCAGCAGAAAGGA
GCTTGAGGGAACACATGGACAATGTGGTGGAGGGTCTTCTCACCCTAACCAAC

Alignment

ORF - retro_rnor_2477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.6 %
• Parental protein coverage: 96.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EIEMATEGDVELELETETSGPERPPEKPRKHDSGAADLERVTDYAEE-KEIQSSNLETAMSVIGDRRSRE
          EIEMATEG.V.L.LE.E.SGPE.PP.KPRKHDSG.ADLERVTD.AEE.KE.QS.NLE.AMS..GDR.SRE
Retrocopy EIEMATEGEVKLKLESEISGPEQPPAKPRKHDSGVADLERVTD*AEE>KETQSLNLEMAMSITGDRQSRE

Parental  QKAKQEREKELAKVTIKKEDLELIMTEMEISRAAAERSLREHMGNVVEALIALTN
          QKAKQE.EKEL.K.TIKKEDLELIMTEMEISRAAAERSLREHM.NVVE.L..LTN
Retrocopy QKAKQEWEKELVKITIKKEDLELIMTEMEISRAAAERSLREHMDNVVEGLLTLTN

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	22.79 RPM
SRP017611_kidney	0.00 RPM	31.05 RPM
SRP017611_liver	0.00 RPM	22.32 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2477 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2477 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2477 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002541	2 retrocopies	retro_cjac_1352, retro_cjac_748,
Echinops telfairi	ENSETEG00000007464	3 retrocopies	retro_etel_1504, retro_etel_1616, retro_etel_1830,
Gorilla gorilla	ENSGGOG00000014809	1 retrocopy	retro_ggor_2557,
Macropus eugenii	ENSMEUG00000013059	1 retrocopy	retro_meug_1583,
Monodelphis domestica	ENSMODG00000017744	2 retrocopies	retro_mdom_26, retro_mdom_306,
Nomascus leucogenys	ENSNLEG00000005454	1 retrocopy	retro_nleu_2150,
Oryctolagus cuniculus	ENSOCUG00000001161	2 retrocopies	retro_ocun_1395, retro_ocun_967,
Otolemur garnettii	ENSOGAG00000010201	1 retrocopy	retro_ogar_1064,
Pongo abelii	ENSPPYG00000006424	1 retrocopy	retro_pabe_3108,
Pan troglodytes	ENSPTRG00000038721	1 retrocopy	retro_ptro_2582,
Rattus norvegicus	ENSRNOG00000015703	1 retrocopy	retro_rnor_2477 ,
Ictidomys tridecemlineatus	ENSSTOG00000006916	2 retrocopies	retro_itri_1861, retro_itri_1864,
Tursiops truncatus	ENSTTRG00000003726	1 retrocopy	retro_ttru_1499,