RetrogeneDB ID: retro_ptro_180

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:106272444..106272896(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSPTRG00000005147
• Aliases: None
• Description: None

Sequence

>retro_ptro_180
GCTGAGGCCTTCAAGGATCTGATGCACAAGTTTCGAAGGGGCCTAGATTTTCTTCATGCCCATTGCATTGTTCACTGATA
TCTGAGGCCAGAGAACATTCTAGTGACAAGTGGTGGGACAGTCAAGCTGGCTGACTTGGTCTGGCCAGCATCTATAGCTA
CCAGATGGCGTTGACACCTGTGGTTGTTACACTCTTTTACTGTGCTCACGAGGTTCTGCAATCTACACAGGCAACATCTG
TGGACATGTGAAGAGTTGGCTGTGTCTTTGCAGAGATGTTTCCTCAAAAGCCTCTCTTCTGTGGAAGCTCTAAAGCCAAC
TAGTTGGGCAAAATCTTTAACCTGATTGGGCTGCCTCTATAGGATGACTGGCCCTAAGATGTGTCTCTACCCCATGGAGC
CTTTCTCCACAGAGGGCCTCACCCAGTGCAGTCGGTGGTGCCTGAGAGGGAG

Alignment

ORF - retro_ptro_180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADF-GLARIYSYQMALTPVVVTLWYRA
          AE..KDLM..F.RGLDFLHA.CIVH..L.PENILVTSGGTVKLAD..GLA.IYSYQMALTPVVVTL.Y.A
Retrocopy AEAFKDLMHKFRRGLDFLHAHCIVH*YLRPENILVTSGGTVKLADL<GLASIYSYQMALTPVVVTLFYCA

Parental  PEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFPPR
          .EVL.QST.AT.VDM..VGC.FAEMF..KPLFCG.S.A..LGKIF.LIGLP..DDWP.DVSLP.GAF..R
Retrocopy HEVL-QSTQATSVDM*RVGCVFAEMFPQKPLFCGSSKAN*LGKIFNLIGLPL*DDWP*DVSLPHGAFLHR

Parental  GPRPVQSVVPEME
          GP.PVQSVVPE.E
Retrocopy GPHPVQSVVPERE

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	18.04 RPM
SRP007412_cerebellum	0.00 RPM	20.58 RPM
SRP007412_heart	0.00 RPM	20.43 RPM
SRP007412_kidney	0.00 RPM	48.35 RPM
SRP007412_liver	0.00 RPM	28.09 RPM
SRP007412_testis	0.00 RPM	18.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_180 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_180 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_275
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,
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 ,
Pan troglodytes	ENSPTRG00000019872	1 retrocopy	retro_ptro_2717,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,