RetrogeneDB ID: retro_ptro_1715

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:177883562..177884023(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HN1
• Ensembl ID: ENSPTRG00000024246
• Aliases: None
• Description: Pan troglodytes hematological and neurological expressed 1 (HN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001048048]

Sequence

>retro_ptro_1715
ATGACCACCACCACCACCTTCAAGGGTGTCAACCCCAACAGCAGGAATATCTCCCGGGTTTTGCGGCTGCCGGGTGGTGG
ATCCAATTTTTCATTGGGTTTTGATGAACCAACAGAACAACCTGTGAGAAAGAACAAAATGTCCTCTAATATCTTTGGGA
CACCTGAAGAAAATCCACCTTCTTGGGCCACATTGGCAGGTGCCAAGTCTAGAGGTGGCGGAGAAGACTTGGAGTCATCT
GGACTGCAGGGAAGGAACGCTTCTGAAGCAAACTCTGTAGATTCTTAGATCTGAAGGAAGAAGATGACATTCATGAAAAT
GTGGACACAGACTTGCAAGGCAGCCTGGGGCCGAGGGAAGAGAAGCCTGCGCCTGCTGCACCTGTGCTGAGCCCTGCGGC
CCCGGCCCCAGCACCATCCATAGGAAATCCCCCTGGTGGCAAGTGCAGCCTCATCCTGGGT

Alignment

ORF - retro_ptro_1715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTTTTFKGVDPNSRNSSRVLRPPGGGSNFSLGFDEPTEQPVRKNKMASNIFGTPEENQASWAKSAGAKS
          MTTTTTFKGV.PNSRN.SRVLR.PGGGSNFSLGFDEPTEQPVRKNKM.SNIFGTPEEN..SWA..AGAKS
Retrocopy MTTTTTFKGVNPNSRNISRVLRLPGGGSNFSLGFDEPTEQPVRKNKMSSNIFGTPEENPPSWATLAGAKS

Parental  SGGREDLESSGLQRRNSSEASSGD-FLDLKGEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVP
          .GG.EDLESSGLQ.RN.SEA.S.D.FLDLK.E.DIHENVDTDL.GSLG..EEKP.PAAPV.SP.APAP.P
Retrocopy RGGGEDLESSGLQGRNASEANSVD<FLDLKEEDDIHENVDTDLQGSLGPREEKPAPAAPVLSPAAPAPAP

Parental  SRRNPPGGKSSLVLG
          S..NPPGGK.SL.LG
Retrocopy SIGNPPGGKCSLILG

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	42.31 RPM
SRP007412_cerebellum	0.00 RPM	43.27 RPM
SRP007412_heart	0.00 RPM	3.82 RPM
SRP007412_kidney	0.00 RPM	24.58 RPM
SRP007412_liver	0.00 RPM	12.47 RPM
SRP007412_testis	0.00 RPM	128.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1715 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1715 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2343
Gorilla gorilla	retro_ggor_1780
Callithrix jacchus	retro_cjac_2715

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014553	1 retrocopy	retro_cjac_2715,
Echinops telfairi	ENSETEG00000013294	1 retrocopy	retro_etel_89,
Homo sapiens	ENSG00000189159	1 retrocopy	retro_hsap_2343,
Gorilla gorilla	ENSGGOG00000013996	1 retrocopy	retro_ggor_1780,
Mustela putorius furo	ENSMPUG00000013971	1 retrocopy	retro_mputfur_1200,
Mus musculus	ENSMUSG00000020737	6 retrocopies	retro_mmus_1096, retro_mmus_2442, retro_mmus_2574, retro_mmus_3706, retro_mmus_864, retro_mmus_934,
Nomascus leucogenys	ENSNLEG00000000610	1 retrocopy	retro_nleu_348,
Oryctolagus cuniculus	ENSOCUG00000002950	2 retrocopies	retro_ocun_1647, retro_ocun_457,
Ochotona princeps	ENSOPRG00000010887	2 retrocopies	retro_opri_537, retro_opri_88,
Pan troglodytes	ENSPTRG00000024246	1 retrocopy	retro_ptro_1715 ,
Rattus norvegicus	ENSRNOG00000003661	2 retrocopies	retro_rnor_1794, retro_rnor_454,
Ictidomys tridecemlineatus	ENSSTOG00000015171	1 retrocopy	retro_itri_1449,