RetrogeneDB ID: retro_ptro_2529

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:54831439..54831971(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNASET2
• Ensembl ID: ENSPTRG00000018796
• Aliases: None
• Description: None

Sequence

>retro_ptro_2529
ATGGTCCAGCACTGGCCTGAGACAGTATGCGAGACAGTTGAAAACGACTGTAGAGACCCTCCGGATTACTGGACAATACA
TGGGACTATGGCCCGATAAAAGTGAAGGATGTAATGGATCGTGGCACTTTAATTTAGAAGAGATTAAGGATCTTTTGCCG
GAAATGAAGGCATAGTGGCCTGATGTAATTCACTCGTTTCCCAATCGTAGCCACTTCTGGAAGCATGAGTGGGAGAAGCA
TGGGACCTCTGCCGCCCTGGTGGACGCACTCAACTCCCAGAAGAAGTACTTTAGCAGAAGCCGGGAACTCTACAGGGAGC
TGGACAGCAACAGTGTGCTCCTAAAACTGCGGCTAAAACCATCCGTCAATTACTACCAAGTTGCAGATTTTAAAGATGCC
CTTGTCAGAGTGTATGGAGTGATACCCAAAATCCAGTGCCTTCCGCGAAGCCAGGATGGGGAAGTACAGACAATTGGTCA
GACAGAACTTTGCCTCACTGAGCAAGGCCAGTAGCTGCAAAACTGCACCGAG

Alignment

ORF - retro_ptro_2529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 69.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVQHWPETVCEKIQNDCRDPPDYWTIHG-LWPDKSEGCNRSWPFNLEEIKDLLPEMRAYWPDVIHSFPNR
          MVQHWPETVCE...NDCRDPPDYWTIHG.LWPDKSEGCN.SW.FNLEEIKDLLPEM.A.WPDVIHSFPNR
Retrocopy MVQHWPETVCETVENDCRDPPDYWTIHG>LWPDKSEGCNGSWHFNLEEIKDLLPEMKA*WPDVIHSFPNR

Parental  SRFWKHEWEKHGTCAAQVDALNSQKKYFGRSLELYRELDLNSVLLKLGIKPSINYYQVADFKDALARVYG
          S.FWKHEWEKHGT.AA.VDALNSQKKYF.RS.ELYRELD.NSVLLKL..KPS.NYYQVADFKDAL.RVYG
Retrocopy SHFWKHEWEKHGTSAALVDALNSQKKYFSRSRELYRELDSNSVLLKLRLKPSVNYYQVADFKDALVRVYG

Parental  VIPKIQCLPPSQDEEVQTIGQIELCLTKQDQQLQNCTE
          VIPKIQCLP.SQD.EVQTIGQ.ELCLT.Q.Q.LQNCTE
Retrocopy VIPKIQCLPRSQDGEVQTIGQTELCLTEQGQ*LQNCTE

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	0.11 RPM	13.33 RPM
SRP007412_cerebellum	0.07 RPM	6.02 RPM
SRP007412_heart	0.06 RPM	3.67 RPM
SRP007412_kidney	0.10 RPM	27.25 RPM
SRP007412_liver	0.20 RPM	22.16 RPM
SRP007412_testis	0.00 RPM	3.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2529 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2529 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2529 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3128

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000003359	1 retrocopy	retro_lafr_764,
Microcebus murinus	ENSMICG00000014184	1 retrocopy	retro_mmur_1544,
Macaca mulatta	ENSMMUG00000005673	1 retrocopy	retro_mmul_1684,
Monodelphis domestica	ENSMODG00000006193	1 retrocopy	retro_mdom_1994,
Nomascus leucogenys	ENSNLEG00000011573	1 retrocopy	retro_nleu_3005,
Pongo abelii	ENSPPYG00000017277	1 retrocopy	retro_pabe_3128,
Pan troglodytes	ENSPTRG00000018796	1 retrocopy	retro_ptro_2529 ,