RetrogeneDB ID: retro_rnor_2459

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:54013956..54015236(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000038453
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2459
ATGTCTGTCAGCGTCAACCGCAGTGTGTCAGACCAGTTCTATCGCTACAAGATGCCCTGTTTGATTGCTAAGGTTGAGGG
CAAAGGAAATGGAATCAAGACAGTTATAGTCAACATGGTTGACGTTGCAAAGGCGCTTAATCGGCCTCCAACGTATCCCA
CCAAATATTTTGTTTGTGAGCTGGGAGCACAGACCCAGTTTGATGTTAAGAATGACCGTTACATTGTCAATGAATCTCAT
GAGGTGAATAAGCGGCAAGACATGTTGGATGGATTCATTAAAAAATTTGTTCTCTGTCCTGAGTGTGAGAATCCTGAAAC
AGATCTGCATGTCAATCCAAAGAAGCAAACAATAGGTAATTCTTGTAAAGCCTGTAGATACCGAGGCATGCTTGACACAC
ATCATAAACTCTGTACATTCATTCTCAAAAACCCCCCTGAGAATAGTGACATTGGTACAGGAAAGAAAGAGAAAGAAAAG
AAAAATAGAAAGGGCAAGGACAAGGAAAATGGCTCTGTATCCACCAGTGAGACACCACCACCTCCACCACCAAATGAAAT
TAGTCCTCCACATGCTGTGGAAGAAGAGGAAGATGATGATTGGGGGGAGGATACAACTGAGGAAGCTCAAAGGCGCAGAA
TGGATGAAATCAGTGACCATGCAAAACGTCTGACACTTAGCGATGATTTGGAAAGAACTGTAGAAGAGCTAACATCCTGT
TTGATTTTGTTAAGAAAAAGAAAGAAGAGGGCATTATTGATTCATCTGATAAAGACATTTCGGCTGAGGCAGAAAGACTG
GATGTAAAAGCCATGGGCCCTCTCGTTTTGACAGAAGTTCTCTTTGATGAGAAGATAAGAGAGCAAATCAAGAAATACAG
GCGCCATTTTTTAAGATTTTGTCATAACAACAAAAAGGCCCAGCGGTACCTTCTTCATGGTTTGGAATGTGTAATAGCAA
TGCATCAAGCTCAGTTGATCTCCAAGATTCCACATATCTTGAAGGAGATGTATGATGCAGACCTTTTAGAGGAAGAGGTC
ATTATCAGCTGGTCAAAAAAGGCCTCTAAGAAATATGTCTCAAAAGAACTTGCCAAAGAGATTCGTGTCAAAGCAGAGCC
ATTTATTAAATGGTTGAAGGAAGCGAAGGAGGAATCTTCTGGTGGTGAGGAAGAAGACGAAGATGAAAATATTGAGGTGG
TATATTCGAAGACTGCCAGTGTACCAAAAGTTGAAACTGTGAAGTCTGACAACAAGGATGACATTGATATTGATGCCATT

Alignment

ORF - retro_rnor_2459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVNVNRSVSDQFYRYKMPRLIAKVEGKGNGIKTVIVNMVDVAKALNRPPTYPTKYFGCELGAQTQFDVK
          MSV.VNRSVSDQFYRYKMP.LIAKVEGKGNGIKTVIVNMVDVAKALNRPPTYPTKYF.CELGAQTQFDVK
Retrocopy MSVSVNRSVSDQFYRYKMPCLIAKVEGKGNGIKTVIVNMVDVAKALNRPPTYPTKYFVCELGAQTQFDVK

Parental  NDRYIVNGSHEANKLQDMLDGFIKKFVLCPECENPETDLHVNPKKQTIGNSCKACGYRGMLDTHHKLCTF
          NDRYIVN.SHE.NK.QDMLDGFIKKFVLCPECENPETDLHVNPKKQTIGNSCKAC.YRGMLDTHHKLCTF
Retrocopy NDRYIVNESHEVNKRQDMLDGFIKKFVLCPECENPETDLHVNPKKQTIGNSCKACRYRGMLDTHHKLCTF

Parental  ILKNPPENSDIGTGKKEKEKKNRKGKDKENGSVSTSETPPPPPPNEISPPHAVEEEEDDDWGEDTTEEAQ
          ILKNPPENSDIGT...........GKDKENGSVSTSETPPPPPPNEISPPHAVEEEEDDDWGEDTTEEAQ
Retrocopy ILKNPPENSDIGTXXXXXXXXXXXGKDKENGSVSTSETPPPPPPNEISPPHAVEEEEDDDWGEDTTEEAQ

Parental  RRRMDEISDHAKGLTLSDDLERTVEERVNILFDFVKK-KKEEGIIDSSDKDIVAEAERLDVKAMGPLVLT
          RRRMDEISDHAK.LTLSDDLERTVEE....L.....K.KKEEGIIDSSDKDI.AEAERLDVKAM......
Retrocopy RRRMDEISDHAKRLTLSDDLERTVEELTSCLI-LLRK<KKEEGIIDSSDKDISAEAERLDVKAMXXXXXX

Parental  EVLFDEKIREQIKKYRRHFLRFCHNNKKAQRYLLHGLECVVAMHQAQLISKIPHILKEMYDADLLEEEVI
          ............KKYRRHFLRFCHNNKKAQRYLLHGLECV.AMHQAQLISKIPHILKEMYDADLLEEEVI
Retrocopy XXXXXXXXXXXXKKYRRHFLRFCHNNKKAQRYLLHGLECVIAMHQAQLISKIPHILKEMYDADLLEEEVI

Parental  ISWSEKASKKYVSKELAKEIRVKAEPFIKWLKEAEEESSGGEEEDEDENIEVVYSKTASVPKVETVKSDN
          ISWS.KASKKYVSKELAKEIRVKAEPFIKWLKEA.EESSGGEEEDEDENIEVVYSKTASVPKVETVKSDN
Retrocopy ISWSKKASKKYVSKELAKEIRVKAEPFIKWLKEAKEESSGGEEEDEDENIEVVYSKTASVPKVETVKSDN

Parental  KDDDIDIDAI
          K.DDIDIDAI
Retrocopy K-DDIDIDAI

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	0.58 RPM	147.39 RPM
SRP017611_kidney	0.63 RPM	175.99 RPM
SRP017611_liver	0.27 RPM	111.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2459 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2459 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,