RetrogeneDB ID: retro_rnor_1781

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:22944847..22946029(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif5
• Ensembl ID: ENSRNOG00000010218
• Aliases: None
• Description: Eukaryotic translation initiation factor 5 [Source:UniProtKB/Swiss-Prot;Acc:Q07205]

Sequence

>retro_rnor_1781
GTTATAGTCAACATGGTTGACTTGCAAAGGCACTTAATCGGCCTCCAATGTATCCCACCAAATATTTGGTTGTGAGTTGG
GAGCACAGACCCAGTTTGATATTAAGAATGATGGTTACATTGTCCGTGGATCTCATGAGGCAAATAAACTGCAAGACATG
TTGGATGGATTCATTAAAAAATTTATTTTCTGTCCTGAGTGTGCGAATCCTGAAACAGATCTGCATGTCAATCCAAAGAA
GCAAACAATAGGTAATTCTTATAAAGCCTGTGCATAGTGAGGCATGCTTGACACACATCATAAACTCTGTACATTCATTC
TCAAAAACCCACCTGAGAATAGTGACACTGGTACAGGAAAGAAGGAAAAAGAAAAGAAAAACTGAAAAGGCAGGGACAAG
GAAAATGGCTCTGTATCCACCAGTGAGACACGACCACCTCCACCACCAAATGAAATTAGTCCTCTACATGCTGTGGAAGA
AGAGGAAGATGATGACTGAGGGGAGGATCCAACTGAGGAAGCTCAAAGGCACAGAATTGATGAAATCAGTGATCATGCAA
AAGGTCTGACACTTAGAGATGATTTGGAAAGAACTGTAGAAGAGTGTGTTAACATCCTGTTTGATTTTGTTAAGAAAAAG
AAAGAAGAGGGCATTATCGATTCATCTGATAAAGACATTGTGGCTGAGGCAAAAAGACAGGATGTAAAAGCCATGGGCCC
TCTTGTTTTGACAGAAGTTCTCCTTGATGAGAAGAAAAGAGAGCAAATCAAGAAATATAGGCGTCATTTCTTAAGATTTT
GTCATAGCACAAAAAGGCCCAGTGGTACCTTCTTCATGGTTTGGAATGTGTGGTAGCAATGCATCAAGCTCAGTTGATCT
ACAAGATTCCACATATCTTGAAGGAGATGTGTGATGCAGACTTTTTAGAGGAAGAGGTCATTATCAGCTGCTCAGAAAAG
GCCTCTAAGAAACATGTCTCAAAGGAACTTACCAAAGAGATTCAGGTCAAAGCAGAGCCATTTATTAAATGGTTGAAGGA
AGCGAAGGAAGAATCTTCTTGTGGGAAGGAAGAAGACGAAGATGAAAATATTGAGGTGGTATATTGGAAGACTGCCAGTG
TACCAAAAGTTGAAACTGTGAAGTCTGACAACAAGGATGATGACATTGATATTGATGCCATT

Alignment

ORF - retro_rnor_1781 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.18 %
• Parental protein coverage: 92.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VIVNMVDV-AKALNRPPTYPTKY-FGCELGAQTQFDVKNDRYIVNGSHEANKLQDMLDGFIKKFVLCPEC
          VIVNMVD..AKALNRPP.YPTKY.FGCELGAQTQFD.KND.YIV.GSHEANKLQDMLDGFIKKF..CPEC
Retrocopy VIVNMVDL<AKALNRPPMYPTKY<FGCELGAQTQFDIKNDGYIVRGSHEANKLQDMLDGFIKKFIFCPEC

Parental  ENPETDLHVNPKKQTIGNSCKACGYRGMLDTHHKLCTFILKNPPENSDIGTGKKEKEKKNRKGKDKENGS
          .NPETDLHVNPKKQTIGNS.KAC...GMLDTHHKLCTFILKNPPENSD.GT.................GS
Retrocopy ANPETDLHVNPKKQTIGNSYKACA**GMLDTHHKLCTFILKNPPENSDTGTXXXXXXXXXXXXXXXXXGS

Parental  VSTSETPPPPPPNEISPPHAVEEEEDDDWGEDTTEEAQRRRMDEISDHAKGLTLSDDLERTVEERVNILF
          VSTSET.PPPPPNEISP.HAVEEEEDDD.GED.TEEAQR.R.DEISDHAKGLTL.DDLERTVEE.VNILF
Retrocopy VSTSETRPPPPPNEISPLHAVEEEEDDD*GEDPTEEAQRHRIDEISDHAKGLTLRDDLERTVEECVNILF

Parental  DFVKKKKEEGIIDSSDKDIVAEAERLDVKAMGPLVLTEVLFDEKIREQIKKYRRHFLRFCHN-NKKAQRY
          DFVKKKKEEGIIDSSDKDIVAEA.R.DVKAMGPLVLTEVL.DEK.REQIKKYRRHFLRFCH...KKAQ.Y
Retrocopy DFVKKKKEEGIIDSSDKDIVAEAKRQDVKAMGPLVLTEVLLDEKKREQIKKYRRHFLRFCHS<HKKAQWY

Parental  LLHGLECVVAMHQAQLISKIPHILKEMYDADLLEEEVIISWSEKASKKYVSKELAKEIRVKAEPFIKWLK
          LLHGLECVVAMHQAQLI.KIPHILKEM.DAD.LEEEVIIS.SEKASKK.VSKEL.KEI.VKAEPFIKWLK
Retrocopy LLHGLECVVAMHQAQLIYKIPHILKEMCDADFLEEEVIISCSEKASKKHVSKELTKEIQVKAEPFIKWLK

Parental  EAEEESSGGEEEDEDENIEVVYSKTASVPKVETVKSDNKDDDIDIDAI
          EA.EESS.G.EEDEDENIEVVY.KTASVPKVETVKSDNKDDDIDIDAI
Retrocopy EAKEESSCGKEEDEDENIEVVYWKTASVPKVETVKSDNKDDDIDIDAI

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	147.39 RPM
SRP017611_kidney	0.00 RPM	175.99 RPM
SRP017611_liver	0.00 RPM	111.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1781 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1781 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1781 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001236	1 retrocopy	retro_cpor_577,
Erinaceus europaeus	ENSEEUG00000015883	1 retrocopy	retro_eeur_288,
Echinops telfairi	ENSETEG00000015220	2 retrocopies	retro_etel_1843, retro_etel_991,
Homo sapiens	ENSG00000100664	1 retrocopy	retro_hsap_4782,
Monodelphis domestica	ENSMODG00000013424	1 retrocopy	retro_mdom_2000,
Nomascus leucogenys	ENSNLEG00000016105	1 retrocopy	retro_nleu_1102,
Pongo abelii	ENSPPYG00000006169	1 retrocopy	retro_pabe_3722,
Pan troglodytes	ENSPTRG00000006753	1 retrocopy	retro_ptro_3183,
Rattus norvegicus	ENSRNOG00000010218	2 retrocopies	retro_rnor_1781 , retro_rnor_2459,
Tursiops truncatus	ENSTTRG00000002384	1 retrocopy	retro_ttru_400,