RetrogeneDB ID: retro_ggor_1318

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:93841165..93841637(+)
• Located in intron of: ENSGGOG00000013694

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTIF3
• Ensembl ID: ENSGGOG00000008409
• Aliases: None
• Description: None

Sequence

>retro_ggor_1318
TCAAAGGAGGCTGCAGAAGACCAGCTCGTGACAGGAACGCAGACCCACCAGGAACGGCTGACGCTGAGAGAGACGGAGAA
GGGTAACCCCAAACCTGGACCACCCCTGACAACGGAACTGACTTTTTCTTCAAACGTTGGACAACATGATTTGGATGCAA
AGACTAAACAGATTCAGCCGTAGATTAAGAAAAAAACACCAAGTTCGAATTACTGTAAAGAAAGCAGAAAATGTAGACGA
GTCAGAAAATGAAGCGGAAGAGATATTTCATCAAATGCTCCAGACTGTGCCTGGAATAGCTACATTCTCATCTAGGCCAC
AAGCTGCTCAAGGAGGAAAAGCTTTAATGTGGGTTCTTTGTCCTTTGAGCAAAAAGGAAGAGAAGGCATATCGAGAAACT
CAAGAGACCCAGGAAAGAGACCCTTTGAACAAAGACCATGGAAATGATAAGGAATCAAATGTTCTGCATCAG

Alignment

ORF - retro_ggor_1318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.95 %
• Parental protein coverage: 56.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STEPAEYQLMTGLQILQERQRLREMEKANPKTGPTLRKELILSSNIGQHDLDTKTKQIQQWIKKK-HLVQ
          S.E.AE.QL.TG.Q..QER..LRE.EK.NPK.GP.L..EL..SSN.GQHDLD.KTKQIQ..IKKK.H.V.
Retrocopy SKEAAEDQLVTGTQTHQERLTLRETEKGNPKPGPPLTTELTFSSNVGQHDLDAKTKQIQP*IKKK>HQVR

Parental  ITIKKGKNVDVSENEMEEIFHQILQTMPGIATFSSRPQAVQGGKALMCVLRALSKNEEKAYKETQETQER
          IT.KK..NVD.SENE.EEIFHQ.LQT.PGIATFSSRPQA.QGGKALM.VL..LSK.EEKAY.ETQETQER
Retrocopy ITVKKAENVDESENEAEEIFHQMLQTVPGIATFSSRPQAAQGGKALMWVLCPLSKKEEKAYRETQETQER

Parental  DTLNKDHGNDKESNVLHQ
          D.LNKDHGNDKESNVLHQ
Retrocopy DPLNKDHGNDKESNVLHQ

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	0.05 RPM	15.30 RPM
SRP007412_cerebellum	0.00 RPM	19.15 RPM
SRP007412_heart	0.03 RPM	9.66 RPM
SRP007412_kidney	0.00 RPM	30.22 RPM
SRP007412_liver	0.00 RPM	21.13 RPM
SRP007412_testis	0.10 RPM	72.62 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1318 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1318 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3284
Pan troglodytes	retro_ptro_2221
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,