RetrogeneDB ID: retro_ggor_275

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:108183874..108184335(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSGGOG00000001404
• Aliases: None
• Description: None

Sequence

>retro_ggor_275
GCTGAGGCCATCAAGGATCTGATGCACAAGTTTCGAAGAGGCCTAGATTTTCTTCATGCCCATTGCATTGTTCACTGATA
TCTGAGGCCAGAGAACATTCTAGTGACAAGTGCTGGGACAGTCAAGCTGGCTGACTTGGTCTGGCCAGCATCTATAGCTA
CCAGATGGCGTTTACACCTGTGGTTGTTACACTCTTGTACTGTGCTCACGAGGTTCTTCTGCAATCTACACAGGCAACAT
CTGTGGACATGTGAAGAGTTGGCTGTGTCTTTGCAGAGATGTTTCCTCAAAAGTCTCTCTTCTGTGGAAGCTCTAAAGCC
AACTAGTTGGGCAAAATCTTTAACCTGATTGGGCTGCCTCTATAGGATGACTGGCCCTAAGATGTGTCTCTACCCCATAG
AACATTTCTCCACAGAGGGCCTCGCCCAGTGCAGTTGGTGGTGCCTGAGATGGAGCACAAC

Alignment

ORF - retro_ggor_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 50.83 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADF-GLARIYSYQMALTPVVVTLWYRA
          AE.IKDLM..F.RGLDFLHA.CIVH..L.PENILVTS.GTVKLAD..GLA.IYSYQMA.TPVVVTL.Y.A
Retrocopy AEAIKDLMHKFRRGLDFLHAHCIVH*YLRPENILVTSAGTVKLADL<GLASIYSYQMAFTPVVVTLLYCA

Parental  PEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFPPR
          .EVLLQST.AT.VDM..VGC.FAEMF..K.LFCG.S.A..LGKIF.LIGLP..DDWP.DVSLP...F..R
Retrocopy HEVLLQSTQATSVDM*RVGCVFAEMFPQKSLFCGSSKAN*LGKIFNLIGLPL*DDWP*DVSLPHRTFLHR

Parental  GPRPVQSVVPEMEES
          GPRPVQ.VVPEME..
Retrocopy GPRPVQLVVPEMEHN

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	20.38 RPM
SRP007412_cerebellum	0.00 RPM	23.72 RPM
SRP007412_heart	0.00 RPM	22.61 RPM
SRP007412_kidney	0.00 RPM	57.20 RPM
SRP007412_liver	0.00 RPM	34.11 RPM
SRP007412_testis	0.00 RPM	31.08 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_275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_275 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_180
Macaca mulatta	retro_mmul_401

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275 ,
Gorilla gorilla	ENSGGOG00000016879	1 retrocopy	retro_ggor_2686,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,