RetrogeneDB ID: retro_ptro_3112

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:53248399..53249221(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSPTRG00000008694
• Aliases: None
• Description: Pan troglodytes eukaryotic translation initiation factor 4A, isoform 1 (EIF4A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001098575]

Sequence

>retro_ptro_3112
TCCATGGATTATAACAGAGAACGTGGCAGCCCAGAGGGAATGGACCCTGATGGTGCCATTGAGAGCAACTGTAATGAGAT
CGTTGATAACTTCGATGATATGAATTTAAAGGAGTCTCTTCTTTGGGGCATCTATGCTTACGATTTTGAGAAGTCTTCTG
CTATTCAGCAGAGAGCTATTATTACCTGTATGAAAGGGTATGATGTGATTGCTCAAGTTCAGTCAGGTACTGGCAAGACA
GCCACATTTGCTATTTCCATCCTGCAACAGTTGGAGACCCAAGCACTAATGCTGGCCCCCACCAGAGAACTGGCTCCACA
GATCCAAAAGGTAATTCTGGCACTTGGAGACTATATGGGAGCAACTTGTCATGTCTGCATTGGTGGAACAAATGTTCAAA
CTGAAATGCAAAAACTGCAGGCTGAAGCACCACATATTGTTGTTGGTACACTTGGGAGAGTGTTTGATATGTTAAACAGA
AGATATCTTTTTCCAAAATGGATCAAAATGCTTGTTTTGGATGAAGCAGATGAAATGTTGAGCCGTGGGTTTAAGGATGA
AATCTATGAGATTTTCCAAAAACTAAATACAAGTATTCAGGTTGTGTTGCTTTCTGCCACAATGCCAACTGATGTGTTGG
AAGTGACCAAAAAATTCATGAGAGATCCAATTTGAATTCTGGTGAAAAAGGAATAATTGACCCTTGAAGGAATCAAACAG
TTTTATATTAATGTTGAGAGAGAAGAATGGAAGTTGGATACACTTTGTGACTTGTACGAGACACTGACCATTACGCAGGC
TGTTATTTTTCTCAAGGCCCAA

Alignment

ORF - retro_ptro_3112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.91 %
• Parental protein coverage: 68.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVI
          S.D.......P.GM.P.G.IESN.NEIVD.FDDMNL.ESLL.GIYAY.FEK.SAIQQRAI..C.KGYDVI
Retrocopy SMDYNRERGSPEGMDPDGAIESNCNEIVDNFDDMNLKESLLWGIYAYDFEKSSAIQQRAIITCMKGYDVI

Parental  AQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAE
          ..AQ...G...T....I.....L....TQAL.LAPTRELA.QIQKV..ALGDYMGA.CH.CIGGTNV..E
Retrocopy --AQVQSGTGKTATFAISILQQLE---TQALMLAPTRELAPQIQKVILALGDYMGATCHVCIGGTNVQTE

Parental  VQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLS
          .QKLQ.EAPHI.VGT.GRVFDMLNRRYL.PK.IKM.VLDEADEMLSRGFKD.IY.IFQKLN...QVVLLS
Retrocopy MQKLQAEAPHIVVGTLGRVFDMLNRRYLFPKWIKMLVLDEADEMLSRGFKDEIYEIFQKLNTSIQVVLLS

Parental  ATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTR
          ATMP.DVLEVTKKFMRDPI.ILVKKE.LTLEGI.QFYINVEREEWKLDTLCDLYETLTITQAVIF....
Retrocopy ATMPTDVLEVTKKFMRDPI*ILVKKE*LTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIFLKAQ

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
SRP007412_brain_prefrontal_cortex	0.20 RPM	108.23 RPM
SRP007412_cerebellum	0.18 RPM	114.43 RPM
SRP007412_heart	0.09 RPM	90.88 RPM
SRP007412_kidney	0.05 RPM	190.54 RPM
SRP007412_liver	0.03 RPM	366.10 RPM
SRP007412_testis	0.00 RPM	114.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3112 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3112 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 66 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,
Pan troglodytes	ENSPTRG00000015718	1 retrocopy	retro_ptro_437,
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,