RetrogeneDB ID: retro_ptro_2597

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:6521091..6521792(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB2
• Ensembl ID: ENSPTRG00000007123
• Aliases: None
• Description: None

Sequence

>retro_ptro_2597
ACAGGAGTTAATTCTAAACCAAAGAGTCATGTGACTATTAGGCATTCCATTTTAGAATAAATTGGAAATAGAGTTATAGC
CAGAGCAGCACAAGTAGCTAAGAAAGCTCAGAACACCAAAGTGCCAGTTCAACCCAGGGAAACAACAAACGTCAACAAAC
AACTGAAACCTACTGCTTCTGTGAAATGGTACAGATGGAAATGTTGGCTCCAAAGGGTCCTTCTCCCATACCTGAGGATG
CCTCCATGAAAGAAGAGAACATCTGCCAAGCTTTTTCTGATGCTTTGCTCTACAAAATTGAGGATATTGATGACAAAGAT
TGGAATAACCCTCAGCTCTGCAGTGACTATGTTAAGGATATCTATCAGTACCTCAGGCAGCTGGAGATTTTGCAGTTCAT
AAACCCACATGTCTTAGATGGATGAGATGTAAATGGACATAAGCATCCCATCCTGGTAGACTGGTTGGTGCAAATCCACT
CCAAGTTGAGGCTTCTTCAGGAGACTCTGTATGTGTGTATTGCCATTATGGATTGATTTTTACTGGTTCAGCCAGTTTCC
CAGAGGAAGCTTCAACTAGTTTGGATTACTGCTCTGCTCTTGGCTTCCAAGTATGAGGAGATGTTTTCTCCAAATATTGA
AGGCTTTGTTTACATCACAGACAATGCTTATACTAGTTCCCAAATCCAAGAAATGGAAACT

Alignment

ORF - retro_ptro_2597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.7 %
• Parental protein coverage: 58.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGVNSKVKSHVTIRRTVLEEIGNRVTTRAAQVAKKAQKTKVPVQPTKTTNVSKQLKPTASVK-PVQMEKL
          TGVNSK.KSHVTIR...LE.IGNRV..RAAQVAKKAQ.TKVPVQP..TTNV.KQLKPTASVK..VQME.L
Retrocopy TGVNSKPKSHVTIRHSILE*IGNRVIARAAQVAKKAQNTKVPVQPRETTNVNKQLKPTASVK<MVQMEML

Parental  APKGPSPTPEDVSMKEENLCQAFSDALLCKIEDIDNEDWENPQLCSDYVKDIYQYLRQLEVLQSVNPHFL
          APKGPSP.PED.SMKEEN.CQAFSDALL.KIEDID..DW.NPQLCSDYVKDIYQYLRQLE.LQ..NPH.L
Retrocopy APKGPSPIPEDASMKEENICQAFSDALLYKIEDIDDKDWNNPQLCSDYVKDIYQYLRQLEILQFINPHVL

Parental  DGRDINGRMRAILVDWLVQVHSKFRLLQETLYMCVGIMDRFLQVQPVSRKKLQLVGITALLLASKYEEMF
          DG.D.NG....ILVDWLVQ.HSK.RLLQETLY.C..IMD.FL.VQPVS..KLQLV.ITALLLASKYEEMF
Retrocopy DG*DVNGHKHPILVDWLVQIHSKLRLLQETLYVCIAIMD*FLLVQPVSQRKLQLVWITALLLASKYEEMF

Parental  SPNIEDFVYITDNAYTSSQIREMET
          SPNIE.FVYITDNAYTSSQI.EMET
Retrocopy SPNIEGFVYITDNAYTSSQIQEMET

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	0.45 RPM
SRP007412_cerebellum	0.00 RPM	1.58 RPM
SRP007412_heart	0.00 RPM	0.70 RPM
SRP007412_kidney	0.08 RPM	0.89 RPM
SRP007412_liver	0.00 RPM	3.63 RPM
SRP007412_testis	0.11 RPM	223.10 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2597 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2597 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2597 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3816
Pongo abelii	retro_pabe_3074

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005269	1 retrocopy	retro_btau_1584,
Homo sapiens	ENSG00000157456	1 retrocopy	retro_hsap_3816,
Nomascus leucogenys	ENSNLEG00000011543	1 retrocopy	retro_nleu_212,
Otolemur garnettii	ENSOGAG00000012885	2 retrocopies	retro_ogar_1770, retro_ogar_2766,
Pongo abelii	ENSPPYG00000006517	2 retrocopies	retro_pabe_3073, retro_pabe_3074,
Pan troglodytes	ENSPTRG00000007123	1 retrocopy	retro_ptro_2597 ,
Ictidomys tridecemlineatus	ENSSTOG00000001275	1 retrocopy	retro_itri_229,
Tarsius syrichta	ENSTSYG00000013818	1 retrocopy	retro_tsyr_1402,