RetrogeneDB ID: retro_ggor_1320

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:2101515..2102082(-)
• Located in intron of: ENSGGOG00000017156

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC90A
• Ensembl ID: ENSGGOG00000002632
• Aliases: None
• Description: None

Sequence

>retro_ggor_1320
TCCTTAGTGGGCTTTCTGGAAGACCATGGGTTTGCTACTCAGCAAGCAGAAATCATTGTGTCTGCATTGGTCAAGGTCCT
GGAGGCCAACGTGGACATCGTCTACAAAGATATGGCCACCAAGATGCAGCAGGAGATCGCTCTTCAGCAAATAATGTCTC
AGACTGTGAATGTGAAAAACGATATGATTACTTTGGAGAAGAGTGAATTTTCAGCCCTCAGAGCAGAACGTGAGAAAATA
AAACTCAAACTACATCAGTTAAAACAAGTAATGGATGAAGTGATTAAAGTCCGAACAGATACTAAATTAGACTTCAACCT
AGAAAAGAGCAGAGTAAAAGAATTGTATTCGTTGAATGAAAAGAAGCTGCTGGAATTGAGAACAGAAATAGTGACATTGC
ATGCCCAGCAAGATCGGGCCGTCACCCAGAGAGATAGGAAGATAGAAACTGAGGATGCTGGCCCCAAAACCATGCTTGAG
TCATACAAGCTTGATAATATTAAATATTTAGCAGGGTCTATATTTACGTGCCTAACAGTAGCTCTGGGATTTTATCACCT
GTGGATC

Alignment

ORF - retro_ggor_1320 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.92 %
• Parental protein coverage: 90.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALVCLLEDNGFATQQAEIIVSALVKILEANMDIVYKDMVTKMQQEITFQQVMSQIANVKKDMIILEKSEF
          .LV..LED.GFATQQAEIIVSALVK.LEAN.DIVYKDM.TKMQQEI..QQ.MSQ..NVK.DMI.LEKSEF
Retrocopy SLVGFLEDHGFATQQAEIIVSALVKVLEANVDIVYKDMATKMQQEIALQQIMSQTVNVKNDMITLEKSEF

Parental  SALRAENEKIKLELHQLKQQVMNPTCTREGEERGVDQNLTHVTCLFQYSLNEKKLLELRTEIVALHAQQD
          SALRAE.EKIKL.LHQLK.QVM.............D.NL........YSLNEKKLLELRTEIV.LHAQQD
Retrocopy SALRAEREKIKLKLHQLK-QVMDEVIKVRTDTK-LDFNLEKSRVKELYSLNEKKLLELRTEIVTLHAQQD

Parental  RALTQTDRKIETEVAGLKTMLESHKLDNIKYLAGSIFTCLTVALGFYRLWI
          RA.TQ.DRKIETE.AG.KTMLES.KLDNIKYLAGSIFTCLTVALGFY.LWI
Retrocopy RAVTQRDRKIETEDAGPKTMLESYKLDNIKYLAGSIFTCLTVALGFYHLWI

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	1.01 RPM	5.80 RPM
SRP007412_cerebellum	0.28 RPM	2.17 RPM
SRP007412_heart	0.28 RPM	1.44 RPM
SRP007412_kidney	2.45 RPM	10.26 RPM
SRP007412_liver	1.16 RPM	5.17 RPM
SRP007412_testis	1.76 RPM	9.84 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_1320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1320 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1795
Pan troglodytes	retro_ptro_1200
Callithrix jacchus	retro_cjac_2522

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000395	2 retrocopies	retro_amel_1628, retro_amel_473,
Canis familiaris	ENSCAFG00000009857	3 retrocopies	retro_cfam_1018, retro_cfam_1556, retro_cfam_823,
Callithrix jacchus	ENSCJAG00000016050	1 retrocopy	retro_cjac_2522,
Cavia porcellus	ENSCPOG00000014899	1 retrocopy	retro_cpor_934,
Equus caballus	ENSECAG00000009150	2 retrocopies	retro_ecab_273, retro_ecab_469,
Felis catus	ENSFCAG00000005972	3 retrocopies	retro_fcat_1290, retro_fcat_1405, retro_fcat_1538,
Homo sapiens	ENSG00000050393	1 retrocopy	retro_hsap_1795,
Gorilla gorilla	ENSGGOG00000002632	1 retrocopy	retro_ggor_1320 ,
Loxodonta africana	ENSLAFG00000003287	2 retrocopies	retro_lafr_1252, retro_lafr_870,
Microcebus murinus	ENSMICG00000000183	2 retrocopies	retro_mmur_280, retro_mmur_580,
Myotis lucifugus	ENSMLUG00000010975	1 retrocopy	retro_mluc_1574,
Mustela putorius furo	ENSMPUG00000000698	1 retrocopy	retro_mputfur_640,
Nomascus leucogenys	ENSNLEG00000000914	1 retrocopy	retro_nleu_2768,
Otolemur garnettii	ENSOGAG00000013458	3 retrocopies	retro_ogar_1587, retro_ogar_1819, retro_ogar_3178,
Pan troglodytes	ENSPTRG00000017740	1 retrocopy	retro_ptro_1200,
Tarsius syrichta	ENSTSYG00000012562	1 retrocopy	retro_tsyr_810,
Tursiops truncatus	ENSTTRG00000012874	1 retrocopy	retro_ttru_1597,