RetrogeneDB ID: retro_pabe_2342

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:122780551..122780955(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3K
• Ensembl ID: ENSPPYG00000025857
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit K [Source:HGNC Symbol;Acc:24656]

Sequence

>retro_pabe_2342
ATAGTGATGTTTTAGCAGATAAGAGTGAGTGTGGGCAAGTTGCTCAACAATATCCACAGGTATAATTCTGAGAACCTGGC
CTCCCTGGGGAGCTATGTGGAGATACAGGCCAAGGAGAATGCCTATGATCTAGAAGCCAACTTGACTGTCCTGAAGCTGT
ACTAGTTCAACCCAGCCTTCTTTAGACCGCAGTCACCACCAAGATTCCACTGAAGGCCTTCACTAACCCATGCCACACCA
ACTTCACCCTGTGCAAGGACATGGTCATCCAAGCACATCAAGAAAAGCAGCCGATCCAACAGATTTTGTACCTGGGGGAT
CTGCTGGAGATTTGACACTTCCAGGCCTTCTGGCAAGCCCTGGATGAAAACATGACCCTTCTGGAAGGTATAACTGGCTT
TGAA

Alignment

ORF - retro_pabe_2342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 76.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAFFQ-TTVTAQI
          ..MF.Q.R..VGKLL..I.RYN.ENLA.L..YVE.QAKENAYDLEANL.VLKLY.FNPAFF..T.VT..I
Retrocopy IVMF*QIRVSVGKLLNNIHRYNSENLASLGSYVEIQAKENAYDLEANLTVLKLY*FNPAFFR<TAVTTKI

Parental  LLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALDENMDLLEGITGFE
          .LKA.TN..HT.FTLCK.M..QAHQE..PI.QILYLGDLLE..HFQAFWQALDENM.LLEGITGFE
Retrocopy PLKAFTNPCHTNFTLCKDMVIQAHQEKQPIQQILYLGDLLEI*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	1.55 RPM
SRP007412_cerebellum	0.00 RPM	2.19 RPM
SRP007412_heart	0.00 RPM	1.32 RPM
SRP007412_kidney	0.00 RPM	2.19 RPM
SRP007412_liver	0.00 RPM	1.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2342 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2342 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2616
Pan troglodytes	retro_ptro_1763
Macaca mulatta	retro_mmul_1478
Macaca mulatta	retro_mmul_1542

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 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,
Rattus norvegicus	ENSRNOG00000020495	3 retrocopies	retro_rnor_1128, retro_rnor_2039, retro_rnor_513,
Sarcophilus harrisii	ENSSHAG00000005313	1 retrocopy	retro_shar_689,
Tarsius syrichta	ENSTSYG00000007001	1 retrocopy	retro_tsyr_1964,