RetrogeneDB ID: retro_rnor_2306

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:89548484..89549701(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046740
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif4a1
• Ensembl ID: ENSRNOG00000030628
• Aliases: None
• Description: eukaryotic initiation factor 4A-I [Source:RefSeq peptide;Acc:NP_955404]

Sequence

>retro_rnor_2306
ATGTCTGCGAGTCAGGATTCTCGACCCAGAGACAATGGCCCCGATGGGATGGAACCGGAAGGCGTCATCGAGAGTAACTG
GAATGAGACTGTGGATAGCTTCGAAGACAAGAACCTCTCAGAATCCCTCCTCCGTGGGATGTATGCCTATGGTTTTGAGA
AGCCCTCTGCCATCCAGCAGCGAGCTATTCTTCCTTGTATCAAGGGTTATGATGTGATTGCTCAAGCCCAGTCTGGGAGT
GGGAAAACAGCTACATTTGCCATATCGATTCTGCAGCAGATTGAATTAGATCTAAAGGCCACTCAGGCTTTGGTTCTGGC
ACCCACTAGTGAATTGGCTCAGCAGATTCAAAAGGTGGTTATGGCATTGGGAGACTATATGGGCGCCTCTTGTCATGCCT
GTATTGAGGGCACCAACGTGCGTGCTGAGGTGCAGAAGCTGCAAATGGAAGCTCCCCATATCATCATGGGCACCCCTGGC
CGGGTGTTCGATATGCTTAACTGGAGATACCTGTCACCCAAATACATCAAGATGTTCGTCCTGGATGAAGCAGATGAAAT
GCTAAGCCGTGGGTTCAAGGATCAGATCTATGATATATTCCAAAAGCTCAACAGCAACACACAGGTAGTTTTGCTGTCTG
CCACAATGCCTTCTGATGTCCTTGAGGTGACTAAGAAGTTCATGAGAGACCCTATTCGGATTCTTGTCAAGAAGGAAGAG
TTGACCCTGGAGGGTATCCGCCAATTCTACATCAATGTGGAACGAGAGGAGTGGAAGCTCGACACATTGTGTGACTTGTA
TGAAACACTGACCATCACCCAGGCAGTAATCCTTATCAACACCAGAAGGAAGGTGGACTGGCTTGCTGAGAAGATGCATG
CCCGGGATTTCACGGTTTCTGCCATGCATGGAGATATGGACCAAAAGGAACGAGACTGATCATGAGGGAGTTCCGGTCTG
GCTCTAGCAGAGTATTAATTACCACTGACCTGTTGGCCAGAGGCATTGATGTGCAGCAGGTCTCCTTAGTCATCAATTAT
GACCTTCCCACCAACAGGGAAAACTATGTCCACAGAATTGGTCGAGGTGGTCAGTTTGGCCGGAAAGGTGTGGCTAGTAA
CATGGTGACAGAAGAAGACAAGAGGACTCTTCGAGACATTGAGACTTTCTACAACACCTCCATTGAAGAGATGCCCCTCA
ACGTTGCTGACCTCATT

Alignment

ORF - retro_rnor_2306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY
          MSASQDSR.RDNGPDGMEPEGVIESNWNE.VDSF.D.NLSESLLRG.YAYGFEKPSAIQQRAILPCIKGY
Retrocopy MSASQDSRPRDNGPDGMEPEGVIESNWNETVDSFEDKNLSESLLRGMYAYGFEKPSAIQQRAILPCIKGY

Parental  DVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNV
          DVIAQAQSG.GKTATFAISILQQIELDLKATQALVLAPT.ELAQQIQKVVMALGDYMGASCHACI.GTNV
Retrocopy DVIAQAQSGSGKTATFAISILQQIELDLKATQALVLAPTSELAQQIQKVVMALGDYMGASCHACIEGTNV

Parental  RAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV
          RAEVQKLQMEAPHII.GTPGRVFDMLN.RYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV
Retrocopy RAEVQKLQMEAPHIIMGTPGRVFDMLNWRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV

Parental  LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFIN
          LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVI.IN
Retrocopy LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVILIN

Parental  TRRKVDWLTEKMHARDFTVSAMHGDMDQKERD-VIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL
          TRRKVDWL.EKMHARDFTVSAMHGDMDQKERD..IMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL
Retrocopy TRRKVDWLAEKMHARDFTVSAMHGDMDQKERD<LIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL

Parental  PTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
          PTNRENY.HRIGRGG.FGRKGVA.NMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
Retrocopy PTNRENYVHRIGRGGQFGRKGVASNMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI

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	0.22 RPM	162.34 RPM
SRP017611_kidney	0.07 RPM	168.73 RPM
SRP017611_liver	0.27 RPM	132.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2306 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2306 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004900	1 retrocopy	retro_cpor_1088,
Erinaceus europaeus	ENSEEUG00000003581	1 retrocopy	retro_eeur_610,
Felis catus	ENSFCAG00000024897	1 retrocopy	retro_fcat_370,
Homo sapiens	ENSG00000161960	10 retrocopies	retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla	ENSGGOG00000024702	8 retrocopies	retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Mus musculus	ENSMUSG00000059796	7 retrocopies	retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Nomascus leucogenys	ENSNLEG00000009547	7 retrocopies	retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Pan troglodytes	ENSPTRG00000008694	10 retrocopies	retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus	ENSRNOG00000001815	2 retrocopies	retro_rnor_1163, retro_rnor_2340,
Rattus norvegicus	ENSRNOG00000030628	3 retrocopies	retro_rnor_1059, retro_rnor_2213, retro_rnor_2306 ,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,
Ictidomys tridecemlineatus	ENSSTOG00000024814	1 retrocopy	retro_itri_610,