RetrogeneDB ID: retro_ptro_52

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL393468.1:1558..2272(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042110
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CDC34
• Ensembl ID: ENSPTRG00000010153
• Aliases: None
• Description: cell division cycle 34 [Source:HGNC Symbol;Acc:1734]

Sequence

>retro_ptro_52
ATGGCCCAGCAGCAGATGACCAGCTCGCAGAAGGCCCTGATGCTCGAGCTGAAATCCCTGCAGGAGGAACCGGTGGAGGG
CTTCCGGATCACCCTGGTGGACGAGTCCGACCTCTACAACTGGGAGGTGGCCATCTTCGGACCCCCCAACACCCTCTACG
AAGGCGGCTACTTCAAGGCGCATATTAAATTTCCTATTGACTACCCCTATTCACCACCTACCTTCAGATTCTTGACCAAA
ATGTGGCACCCCAACATTTATGAGAATGGAGATGTATGCATTTCGATTCTTCATCCGCCTGTAGATGACCCACAGAGTGG
AGAACTGCCTTCTGAAAGGTGGAATCCTACTCAGAATGTGAGGACTATCCTATTAAGTGTAATCTCACTGCTTAATGAGC
CCAACACCTTCTCCCCAGCCAATGTCGATGCTTCAGTTATGTTCAGGAAATGGAGAGACAGTAAAGGAAAAGACAAAGAA
TATGCTGAAATTATTAGGAAACAAGTTTCAGCCACTAAGGCCGAAGCAGAAAAGGATGGAGTGAAGGTCCCCACAACCCT
GGCGGAATACTGCATCAAAACTAAAGTGCCTTCCAATGACAACAGCTCAGATTTGCTTTACGACGACTTGTATGATGACG
ACATTGATGATGAAGATGAGGAGGAGGAAGATGCCGACTGTTATGATGATGATGATTCTGGGAATGAGGAGTCG

Alignment

ORF - retro_ptro_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARPLVPSSQKALLLELKGLQEEPVEGFRVTLV-EGDLYNLEVAIFGPPNTYYEGGYFKARLKFPIDYPY
          MA.....SSQKAL.LELK.LQEEPVEGFR.TLV.E.DLYN.EVAIFGPPNT.YEGGYFKA..KFPIDYPY
Retrocopy MAQQQMTSSQKALMLELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYFKAHIKFPIDYPY

Parental  SPPAFRFLTKMWHPNIYETGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPA
          SPP.FRFLTKMWHPNIYE.GDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPA
Retrocopy SPPTFRFLTKMWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPA

Parental  NVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKTKAPAPDEGSDLFYDDY
          NVDASVM.RKW..SKGKD.EY..IIRKQV..TK..AE.DGVKVPTTLAEYC.KTK.P..D..SDL.YDD.
Retrocopy NVDASVMFRKWRDSKGKDKEYAEIIRKQVSATKAEAEKDGVKVPTTLAEYCIKTKVPSNDNSSDLLYDDL

Parental  YED---GEVEEAGSCFGEDEDDSGTEES
          Y.D....E.EE.......D.DDSG.EES
Retrocopy YDDDIDDEDEEEEDADCYDDDDSGNEES

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	3.84 RPM	58.31 RPM
SRP007412_cerebellum	6.13 RPM	55.71 RPM
SRP007412_heart	8.13 RPM	16.61 RPM
SRP007412_kidney	5.75 RPM	42.92 RPM
SRP007412_liver	6.58 RPM	74.08 RPM
SRP007412_testis	37.09 RPM	62.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_52 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_52 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_52 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023874	1 retrocopy	retro_cpor_743,
Macropus eugenii	ENSMEUG00000000812	1 retrocopy	retro_meug_1683,
Mus musculus	ENSMUSG00000020307	1 retrocopy	retro_mmus_23,
Ochotona princeps	ENSOPRG00000001017	1 retrocopy	retro_opri_464,
Pan troglodytes	ENSPTRG00000010153	1 retrocopy	retro_ptro_52 ,
Ictidomys tridecemlineatus	ENSSTOG00000023255	1 retrocopy	retro_itri_822,
Tursiops truncatus	ENSTTRG00000000391	2 retrocopies	retro_ttru_1142, retro_ttru_98,