RetrogeneDB ID: retro_ptro_810

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:28201329..28202484(+)
• 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_810
ATGTCTGCAAGTCAGGATTCCTGATCCAGAGACAATGGCCCTGATGGGATGGAGCCCAAAGGTGTCATCGAGAGTAACTG
GAATGAGATTGTTGACAGCTTTGATGACATGAACCTCTTGGAGTCCCTTCTCCATGGCATCTACGCCTATGGTTCTGAGA
AGCCCTCTGCCATCCAGCAGCGAGCCATTCTACCTTGTATCAGGGGTTATGTTGTGATCGTTCAAGCCCAATCTGGCACT
GGGAAAATGGCCACATTTTCCATATCAATTCTGCATCAGATTGAATTAGATGTAAAAGCCACCCAGGCCTTGGTCCTAGC
ACCCACTTGAGAATCGGCTCAGCAGATACAGAAGGTGGTCATAGCACTAGGAGACCACCTGGGTGCCTCCTGTCACACCT
GTATTGGGGGCACCAACGTTCGTGCTGAGGTACAGAAACTGCAGATGGAAGCTCCCCATATAATTGTGGGTACCCCTGGC
CATGTGTTTGATATGCTTAACTGGAGATACCTGTCTCCCAAATACATCAAGTTGTTTGTACTGGACAAAGCTGACGAAAT
GTTAAGCCATGGATTCAAGGACCAGATCTATGACATATTCCAAGAGCTCAACAGCAACACCCAGGTAGTTTTGCCATCAG
CTACAATGCCTTCTGATGTGCTTGAGGTGACCAAGAAGTTCATGAGGGAACAGATTTGGATTCTGGTCAAGAAGGAAGAG
TTGACCCTGGAGGGTATCTGCCAATTCTACATCAACATGGAACGAGAAGAGTGGAAGCTGGACACACTGTGTGACTTGTA
TGAAACCCTGACCATCACCCAGGCAGTCATCTTCCTCAACACCCGCAGGAAGGTGGACTGGCTTACCAAGAAGATGCATG
CTCAAGATTTCACTGTCTCTGCCATGCATGGAGATATGGACCAGAAGGAATGAGACGGGATCATGAGGGAGTTTCATTCT
GGCTCTAGCAGAGTTTTGATTATCACTGACCTGCTGGTCAGAGGCATTGATGTGCAGCAGGTTTCTTTAGTCATCAACTA
TGACCTTCCCACCAACAGGGAAAACTATATCCACAGAATCGGTTGACGTGGACAGTTTGGCCGTAAAGGTGTGGCTATTA
ACATGGTGACAGAAGAAGACAAGAGGACTCTGAGA

Alignment

ORF - retro_ptro_810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.35 %
• Parental protein coverage: 94.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY
          MSASQDS.SRDNGPDGMEP.GVIESNWNEIVDSFDDMNL.ESLL.GIYAYG.EKPSAIQQRAILPCI.GY
Retrocopy MSASQDS*SRDNGPDGMEPKGVIESNWNEIVDSFDDMNLLESLLHGIYAYGSEKPSAIQQRAILPCIRGY

Parental  DVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNV
          .VI.QAQSGTGK.ATF.ISIL.QIELD.KATQALVLAPT.E.AQQIQKVV.ALGD..GASCH.CIGGTNV
Retrocopy VVIVQAQSGTGKMATFSISILHQIELDVKATQALVLAPT*ESAQQIQKVVIALGDHLGASCHTCIGGTNV

Parental  RAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV
          RAEVQKLQMEAPHIIVGTPG.VFDMLN.RYLSPKYIK.FVLD.ADEMLS.GFKDQIYDIFQ.LNSNTQVV
Retrocopy RAEVQKLQMEAPHIIVGTPGHVFDMLNWRYLSPKYIKLFVLDKADEMLSHGFKDQIYDIFQELNSNTQVV

Parental  LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFIN
          L.SATMPSDVLEVTKKFMR..I.ILVKKEELTLEGI.QFYIN.EREEWKLDTLCDLYETLTITQAVIF.N
Retrocopy LPSATMPSDVLEVTKKFMREQIWILVKKEELTLEGICQFYINMEREEWKLDTLCDLYETLTITQAVIFLN

Parental  TRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP
          TRRKVDWLT.KMHA.DFTVSAMHGDMDQKE.D.IMREF.SGSSRVLI.TDLL.RGIDVQQVSLVINYDLP
Retrocopy TRRKVDWLTKKMHAQDFTVSAMHGDMDQKE*DGIMREFHSGSSRVLIITDLLVRGIDVQQVSLVINYDLP

Parental  TNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLR
          TNRENYIHRIG..G.FGRKGVAINMVTEEDKRTLR
Retrocopy TNRENYIHRIG*RGQFGRKGVAINMVTEEDKRTLR

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	0.09 RPM	108.23 RPM
SRP007412_cerebellum	0.04 RPM	114.43 RPM
SRP007412_heart	0.17 RPM	90.88 RPM
SRP007412_kidney	0.10 RPM	190.54 RPM
SRP007412_liver	0.23 RPM	366.10 RPM
SRP007412_testis	0.11 RPM	114.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_810 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_810 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1182
Pongo abelii	retro_pabe_987

---

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,