RetrogeneDB ID: retro_ptro_2221

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:530297..530768(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTIF3
• Ensembl ID: ENSPTRG00000005732
• Aliases: None
• Description: mitochondrial translational initiation factor 3 [Source:HGNC Symbol;Acc:29788]

Sequence

>retro_ptro_2221
TCAAAGGAGGCTGCAGAAGACCAGCTCGTGACAGGAAAGCAGACCCACCAGCAATGGCCGAGGCTGAGAGAGACGGAGAA
GGGTAACCCCAAACCTGGACCAGCCCTGACAACGGAACTGACTTTTTCTTCAAACGTTGGACAACATGATTTGGATGCAA
AGACTAAACAGATTCAGCCGTGGATTAAGAAAAAACACCAAGTTCGAATTACCGTAAAGAAAGCAGAAAATGTAGACGAG
TCAGAAAATAAAGTGGAGGAGATATTTCATCAAATACTCCAGACTGTGCCTGGAATAGCTACGTTCTCATCTAGGCCACA
AGCTGTCCAAGGAGGAAAAGCTTTAATGTGGGTTCTTTGTCCTTTGAGCAAAAAGGAAGAGAAGGCGTATCGAGAAACTC
AAGAGACCCAGGAAAGAGACCCTTTGAACAAAGACCATGGAAATGATAAGGAATCAAATGTTCTGCATCAG

Alignment

ORF - retro_ptro_2221 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.07 %
• Parental protein coverage: 56.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STEPAEYQLMTGLQILQERQRLREMEKANPKTGPTLRKELILSSNIGQHDLDTKTKQIQQWIKKKHLVQI
          S.E.AE.QL.TG.Q..Q...RLRE.EK.NPK.GP.L..EL..SSN.GQHDLD.KTKQIQ.WIKKKH.V.I
Retrocopy SKEAAEDQLVTGKQTHQQWPRLRETEKGNPKPGPALTTELTFSSNVGQHDLDAKTKQIQPWIKKKHQVRI

Parental  TIKKGKNVDVSENEMEEIFHQILQTMPGIATFSSRPQAVQGGKALMCVLRALSKNEEKAYKETQETQERD
          T.KK..NVD.SEN..EEIFHQILQT.PGIATFSSRPQAVQGGKALM.VL..LSK.EEKAY.ETQETQERD
Retrocopy TVKKAENVDESENKVEEIFHQILQTVPGIATFSSRPQAVQGGKALMWVLCPLSKKEEKAYRETQETQERD

Parental  TLNKDHGNDKESNVLHQ
          .LNKDHGNDKESNVLHQ
Retrocopy PLNKDHGNDKESNVLHQ

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	0.02 RPM	12.60 RPM
SRP007412_cerebellum	0.00 RPM	12.65 RPM
SRP007412_heart	0.00 RPM	35.03 RPM
SRP007412_kidney	0.00 RPM	24.92 RPM
SRP007412_liver	0.00 RPM	9.85 RPM
SRP007412_testis	3.48 RPM	79.88 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2221 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2221 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3284
Gorilla gorilla	retro_ggor_1318
Pongo abelii	retro_pabe_2713

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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,