RetrogeneDB ID: retro_pabe_2713

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:348244..348715(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTIF3
• Ensembl ID: ENSPPYG00000005236
• Aliases: None
• Description: mitochondrial translational initiation factor 3 [Source:HGNC Symbol;Acc:29788]

Sequence

>retro_pabe_2713
TCAAAGGAGCCTGCAGAAGACCAGCTCATGACAGGAATGCAGACCCACCGGGAATGGCTGAGGCTGAGAGAGACGGAGAA
GGGTAACCCCAAACCTGGACCAACGCTGACAAAAGAACCGACTTTATCTTCAAACTTTGGACAACATGATTTGGATGCAA
AGACTAAACAGATTCAGCCGTGGATTAAGAAAAAACACCAAGTTCGAATTACTATAAAGAAAGGAGAAAATATAGATGAG
TCAGAAAATAAAGTGGAGGAGATATTTCATCAAATACTCCAGACTGTGCCTGGAATAGCTACATTCTCATCTAGGCCACA
AGCTGTTCAAGGACGAAAAGCTTTAATGTGGGTTCTTCGTCCTTTGAGCAAAAAGGAAGAGAAGGCATATCGAGAAACTC
AAGAGACCCAGGAAAGAGACACTTTGAACAAAGACCATGGAAATGATAAGGAATCAAATGTTCTGCATCAG

Alignment

ORF - retro_pabe_2713 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.98 %
• Parental protein coverage: 56.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STEPAEYQLMTGLQIFQEQQRLREMEKASPKTGPTVRKELILSSNIGQHDLDTKTKQIQQWIKKKHLVQI
          S.EPAE.QLMTG.Q...E..RLRE.EK..PK.GPT..KE..LSSN.GQHDLD.KTKQIQ.WIKKKH.V.I
Retrocopy SKEPAEDQLMTGMQTHREWLRLRETEKGNPKPGPTLTKEPTLSSNFGQHDLDAKTKQIQPWIKKKHQVRI

Parental  TIKKGKNVDVSENEMEEIFHQILQTMPGIATFSSKPQAVRG-KALMCVLRALSKNEEKAYRETQETQERD
          TIKKG.N.D.SEN..EEIFHQILQT.PGIATFSS.PQAV.G.KALM.VLR.LSK.EEKAYRETQETQERD
Retrocopy TIKKGENIDESENKVEEIFHQILQTVPGIATFSSRPQAVQGRKALMWVLRPLSKKEEKAYRETQETQERD

Parental  TLNKDHGNDKESNVLHQ
          TLNKDHGNDKESNVLHQ
Retrocopy TLNKDHGNDKESNVLHQ

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	8.57 RPM
SRP007412_cerebellum	0.00 RPM	11.92 RPM
SRP007412_heart	0.00 RPM	14.99 RPM
SRP007412_kidney	0.00 RPM	8.52 RPM
SRP007412_liver	0.00 RPM	8.05 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2713 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2713 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2713 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3284
Pan troglodytes	retro_ptro_2221
Gorilla gorilla	retro_ggor_1318

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004404	1 retrocopy	retro_chof_466,
Homo sapiens	ENSG00000122033	1 retrocopy	retro_hsap_3284,
Gorilla gorilla	ENSGGOG00000008409	1 retrocopy	retro_ggor_1318,
Nomascus leucogenys	ENSNLEG00000000343	1 retrocopy	retro_nleu_1350,
Oryctolagus cuniculus	ENSOCUG00000011721	1 retrocopy	retro_ocun_533,
Pongo abelii	ENSPPYG00000005236	1 retrocopy	retro_pabe_2713 ,
Pan troglodytes	ENSPTRG00000005732	1 retrocopy	retro_ptro_2221,
Tupaia belangeri	ENSTBEG00000012276	3 retrocopies	retro_tbel_4048, retro_tbel_4602, retro_tbel_760,