RetrogeneDB ID: retro_ptro_1763

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:24956214..24956619(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3K
• Ensembl ID: ENSPTRG00000010934
• Aliases: EIF3K, EIF3S12
• Description: Eukaryotic translation initiation factor 3 subunit K [Source:UniProtKB/TrEMBL;Acc:H2QG88]

Sequence

>retro_ptro_1763
ATAGCGATGTTTTAGTAGTTGAGAGTGAATGTGGGCAAGTTGCTCAACAATATCCACAGGTATAATTCTGAGAACCTGGC
CTCCCTGGGGAGCTATGTGGAGATACAGGCCAAGGAGAATGCCTGTGATCTAGAAGCCAGCTTGACTGTCCTGAAGCTGT
ACTAGTTCAACCCAGCCTTCTTTCAGACCACGGTCACCACCCAGATCCCACTGAAGGCCTTTACCAACCCATGCCACACC
AGCTTCACCCTGTGCAAGCACATGGTCATCCAAGTGCATCAAGAAAAGCAGCTGATCCAACAGATTTTGTACCTGGGAGA
TCTGCTGGAGACTTGACACTTCCAGGCCTTCTGGCAAGCCCTGGATGAAAACATGACCCTTTTGGAAGGTATAACTGGCT
TTGAA

Alignment

ORF - retro_ptro_1763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.56 %
• Parental protein coverage: 61.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAFFQTTVTAQIL
          .AMF...R.NVGKLL..I.RYN.ENLA.L..YVE.QAKENA.DLEA.L.VLKLY.FNPAFFQTTVT.QI.
Retrocopy IAMF**LRVNVGKLLNNIHRYNSENLASLGSYVEIQAKENACDLEASLTVLKLY*FNPAFFQTTVTTQIP

Parental  LKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALDENMDLLEGITGFE
          LKA.TN..HT.FTLCK.M..Q.HQE...I.QILYLGDLLET.HFQAFWQALDENM.LLEGITGFE
Retrocopy LKAFTNPCHTSFTLCKHMVIQVHQEKQLIQQILYLGDLLET*HFQAFWQALDENMTLLEGITGFE

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	0.00 RPM	76.43 RPM
SRP007412_cerebellum	0.00 RPM	52.70 RPM
SRP007412_heart	0.00 RPM	40.43 RPM
SRP007412_kidney	0.03 RPM	105.10 RPM
SRP007412_liver	0.03 RPM	58.95 RPM
SRP007412_testis	0.00 RPM	30.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1763 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1763 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1763 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2616
Pongo abelii	retro_pabe_2342
Macaca mulatta	retro_mmul_1478
Macaca mulatta	retro_mmul_1542

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007594	3 retrocopies	retro_etel_1653, retro_etel_1868, retro_etel_5,
Homo sapiens	ENSG00000178982	2 retrocopies	retro_hsap_2616, retro_hsap_3224,
Gorilla gorilla	ENSGGOG00000016808	1 retrocopy	retro_ggor_2192,
Myotis lucifugus	ENSMLUG00000010217	1 retrocopy	retro_mluc_645,
Macaca mulatta	ENSMMUG00000028767	2 retrocopies	retro_mmul_1478, retro_mmul_2029,
Monodelphis domestica	ENSMODG00000013314	3 retrocopies	retro_mdom_1235, retro_mdom_1929, retro_mdom_781,
Otolemur garnettii	ENSOGAG00000026260	1 retrocopy	retro_ogar_413,
Pongo abelii	ENSPPYG00000025857	4 retrocopies	retro_pabe_2342, retro_pabe_2555, retro_pabe_2610, retro_pabe_2673,
Pan troglodytes	ENSPTRG00000010934	2 retrocopies	retro_ptro_1763 , retro_ptro_2176,
Sarcophilus harrisii	ENSSHAG00000005313	1 retrocopy	retro_shar_689,
Tarsius syrichta	ENSTSYG00000007001	1 retrocopy	retro_tsyr_1964,