RetrogeneDB ID: retro_ptro_450

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:91678148..91678988(+)
• Located in intron of: ENSPTRG00000002753

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_450
TCCAGAGACAATGGTCCTGATGAGATGGAGCCTGAAGGCATCATTGAGAGAAACTGAAATGAGATTGTTGACAGTTTTGA
TGATATGAACCTCTTGGAATCCCTCCTCCATGGCATCTATGCCTATGGTTTTGAGAAGTCCTCTGCCAACCAGTAGCGAG
CCATTCTTCTTGTATCAAGGATTATGATGTGATCACTCAAGCCCTATCTGGGACTGGGAAAATGGCCACTTTTGCCATAT
CAATTCTGCAGTAGATTGAATTAGATCTGAAGGCTACCCACACCTTGGTCCCAGCATCCACTTGATAATTGGCTCAAAAG
ATAGAAAAGGTGGTCATGACACTAGGAGACTACATGGGTGCCTCCTGTCATGGCTGTATTGGGGGCACCAACGTGCATGC
TGAGGTGCAGAAACTACAGATGGAAGTTCCCCATATCATCGTGGGTACCCCTGGCCATATGTCTGATATGCTTAACCAGA
GATACCTGTCTCCCAAATACATCAAGATGTTTGTACTGGATGAAGCTGATGAAATGTTAAGCCATGGATTCAAGGACTCA
ATCTATGACATATTCCAAAAGCTCAACAGCAACACCCAGGTGGTTTTGCTATCAGCCACAAGGCCTTCTGATGTGCTTGA
GGTGACCAAGAAGTTCATGAGGGACCCCATTTGGATTCCTGTCAAGAAGGAAGAGTTGACCCTGGAGGGGGTCCACCAAT
TCTACATCAATGTGGAACATGAGGAGTGGAAACTGAGCACACTGTGTGGTTTGTATGAAACCCTGATTGTCACCCTAGGC
AGTCATCTTCATCAATACTGGAAAGAAGGTGGATTGGCTC

Alignment

ORF - retro_ptro_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.98 %
• Parental protein coverage: 68.97 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAIL-PCIKGYDVIAQAQ
          SRDNGPD.MEPEG.IE.N.NEIVDSFDDMNL.ESLL.GIYAYGFEK.SA.Q.RAIL..CIK.YDVI.QA.
Retrocopy SRDNGPDEMEPEGIIERN*NEIVDSFDDMNLLESLLHGIYAYGFEKSSANQ*RAIL<SCIKDYDVITQAL

Parental  SGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKL
          SGTGK.ATFAISILQ.IELDLKAT..LV.A.T..LAQ.I.KVVM.LGDYMGASCH.CIGGTNV.AEVQKL
Retrocopy SGTGKMATFAISILQ*IELDLKATHTLVPAST**LAQKIEKVVMTLGDYMGASCHGCIGGTNVHAEVQKL

Parental  QMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMP
          QME.PHIIVGTPG...DMLN.RYLSPKYIKMFVLDEADEMLS.GFKD.IYDIFQKLNSNTQVVLLSAT.P
Retrocopy QMEVPHIIVGTPGHMSDMLNQRYLSPKYIKMFVLDEADEMLSHGFKDSIYDIFQKLNSNTQVVLLSATRP

Parental  SDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQ-AVIFINTRRKVD
          SDVLEVTKKFMRDPI.I.VKKEELTLEG..QFYINVE.EEWKL.TLC.LYETL..T..AVIFINT..KVD
Retrocopy SDVLEVTKKFMRDPIWIPVKKEELTLEGVHQFYINVEHEEWKLSTLCGLYETLIVTL>AVIFINTGKKVD

Parental  WL
          WL
Retrocopy WL

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	0.05 RPM	108.23 RPM
SRP007412_cerebellum	0.22 RPM	114.43 RPM
SRP007412_heart	0.00 RPM	90.88 RPM
SRP007412_kidney	0.05 RPM	190.54 RPM
SRP007412_liver	0.00 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_450 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_450 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_610
Gorilla gorilla	retro_ggor_537
Pongo abelii	retro_pabe_548

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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,