RetrogeneDB ID: retro_ptro_1735

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:208435518..208436255(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF207
• Ensembl ID: ENSPTRG00000008989
• Aliases: None
• Description: None

Sequence

>retro_ptro_1735
TCACCAGGTATCCCCTCCACTCCCCGACCCCCATTCCACATCCTAGAATTCCTCCAGTGACCCAAACACAGGCTGTTTCA
GCGCCAGGTATTCTTAACAGACCACCTGCAGCAACAGCAACTGTACCTGCTCCACAGCCTCCAGTTACCAAGCCTCTTTT
CTCCAGTGCTGGACAGGCTCAGGCAGCTGTCCAAGGACCTGTTGGTACAGATTTCAAACCCTTAAATAGTACCCCTGAAG
CAACTGCGGCATCCCCAAAGCCTATATTCTCTGCTTATACACAGTCTGCAGATTCAACCACTAGTACAACAAATAGTACT
GCAGCTAAACCAGCAGCTTCAATAACAAGTAAGCCTGCTACACTTGTAACAACCAATGCAACCAGTAAGTTGATCCATCC
AGATGAGGGTATATATCTGGAAGAGAGAAGGGCACAGTTACCTAGAGATCAACATAATCTTCCTCTGCAAGGAGAGGCCC
CCATCGGTAATCCACCAGTTGGACCAATTGGAGGTATGACGCCACCATAGCCAGGCATCCCACAGCAACAAGGAGTGAGA
CCCCCAGTGCCGCCTCATGGTCAATATGGTGGTCATCATCAAGCCATGCCAGCATACCTTCCTGGTGCTATCCCCCCATA
TGGGCAGGGACCGCCAACAGTGCCCCCTTACCAGAGCGGGCCTCCTCGACCTCCAATGGGAATGAGACCTCCTGTAATGC
TGCAAGGTGGCCAGTAC

Alignment

ORF - retro_ptro_1735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 50.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APGILNRP-PAPTATVPAPQ-PPVTKPLFPSA-GQMGTPVTSSSTASSNSESLSASSKALFPSTAQAQAA
          .PGI...P.P.P....P.P..PPVT.....SA.G....P.....T............K.LF.S..QAQAA
Retrocopy SPGIPSTP<PTP---IPHPRIPPVTQTQAVSAPGILNRPPAATATVPAPQPPVT---KPLFSSAGQAQAA

Parental  VQGPVGTDFKPLNSTPATTTEPPKPTFPAYTQSTASTTSTTNSTAAKPAASITSKPATLTTTSATSKLIH
          VQGPVGTDFKPLNSTP..T...PKP.F.AYTQS..STTSTTNSTAAKPAASITSKPATL.TT.ATSKLIH
Retrocopy VQGPVGTDFKPLNSTPEATAASPKPIFSAYTQSADSTTSTTNSTAAKPAASITSKPATLVTTNATSKLIH

Parental  PDEDISLEERRAQLPKYQRNLPRPGQAPIGNPPVGPIGGMMPPQPGIPQQQGMRPPMPPHGQYGGHHQGM
          PDE.I.LEERRAQLP..Q.NLP..G.APIGNPPVGPIGGM.PP.PGIPQQQG.RPP.PPHGQYGGHHQ.M
Retrocopy PDEGIYLEERRAQLPRDQHNLPLQGEAPIGNPPVGPIGGMTPP*PGIPQQQGVRPPVPPHGQYGGHHQAM

Parental  PGYLPGAMPPYGQGPPMVPPYQGGPPRPPMGMRPPVMSQGGRY
          P.YLPGA.PPYGQGPP.VPPYQ.GPPRPPMGMRPPVM.QGG.Y
Retrocopy PAYLPGAIPPYGQGPPTVPPYQSGPPRPPMGMRPPVMLQGGQY

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	49.35 RPM
SRP007412_cerebellum	0.07 RPM	65.21 RPM
SRP007412_heart	0.03 RPM	42.15 RPM
SRP007412_kidney	0.13 RPM	78.27 RPM
SRP007412_liver	0.07 RPM	58.17 RPM
SRP007412_testis	0.21 RPM	106.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1735 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1735 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2373

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001728	1 retrocopy	retro_cpor_1464,
Echinops telfairi	ENSETEG00000003828	1 retrocopy	retro_etel_883,
Homo sapiens	ENSG00000010244	1 retrocopy	retro_hsap_2373,
Myotis lucifugus	ENSMLUG00000016085	1 retrocopy	retro_mluc_322,
Nomascus leucogenys	ENSNLEG00000005954	1 retrocopy	retro_nleu_362,
Otolemur garnettii	ENSOGAG00000001200	2 retrocopies	retro_ogar_33, retro_ogar_751,
Pongo abelii	ENSPPYG00000008161	1 retrocopy	retro_pabe_2144,
Pan troglodytes	ENSPTRG00000008989	1 retrocopy	retro_ptro_1735 ,
Ictidomys tridecemlineatus	ENSSTOG00000000712	2 retrocopies	retro_itri_1800, retro_itri_1875,