RetrogeneDB ID: retro_ptro_2285

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:110266855..110267422(-)
• Located in intron of: ENSPTRG00000017122

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000041730
• Aliases: None
• Description: None

Sequence

>retro_ptro_2285
ATGACTGATAAAGCAGAGAAGGTTGCTGTAGAACCTGAAAATGTGTTTAAACGTCCCAGGGAATCTGAGAGTCCTTCATC
TCAGAAAAGGCAGAAGATGGCCCTGTTGTTAAGGAAACAAAGAGCAGGAGACAGCCTTATTGGAGGCTCTGCCATGTCCA
AGGAAAAGAAGCTTATGGCAGGAGATGGTATTCCACCAAGCCAACTGGATTCTCGGTTTGATGACTTCAGTGGTTGCAGC
AAAGATGGGCTGATGCAGAAACCTGGTAGAAATGCACCTGTAGGAGGAATCATTACCAGCAATTTCTCTGGAGATGACCT
AAAAGTCACAGAAATGCTCCCTTTTCCAAAATGTCAAGAAGAAATTAATGCTGATATAAAATGTCAATTAGTGAAGGAAA
TTCAACACTTTAGACGAAAATATGAAAAACTCTTCAAATTGCTTGAAGGACTGCAAGGACCTATAGAAGTCAAGAAATGA
TTTTTTGAATCCATCATCAAGGAAGCCACAAGATTTATGAGACGAGACTTAATTCAGCACCTTGAGAAGAAACTGGAACA
AATGATT

Alignment

ORF - retro_ptro_2285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTDKTEKVAVDPETVFKRPRECDSPSYQKRQRMALLARKQGAGDSLIAGSAMSKEKKLMTGDGIPPSQLD
          MTDK.EKVAV.PE.VFKRPRE..SPS.QKRQ.MALL.RKQ.AGDSLI.GSAMSKEKKLM.GDGIPPSQLD
Retrocopy MTDKAEKVAVEPENVFKRPRESESPSSQKRQKMALLLRKQRAGDSLIGGSAMSKEKKLMAGDGIPPSQLD

Parental  SQIDDFTGFSKDGMMRKPGSNAPVGGNVTSSFSGDDLECRGIASSPKSQQEINADIKYQVVKEIRYLGRK
          S..DDF.G.SKDG.M.KPG.NAPVGG..TS.FSGDDL........PK.Q.EINADIK.Q.VKEI....RK
Retrocopy SRFDDFSGCSKDGLMQKPGRNAPVGGIITSNFSGDDLKVTEMLPFPKCQEEINADIKCQLVKEIQHFRRK

Parental  YEKVFKMLEGVQGPTAVRKRFFESIIKEAARCMRRDFVKHLKKKLKRMI
          YEK.FK.LEG.QGP..V.K.FFESIIKEA.R.MRRD...HL.KKL..MI
Retrocopy YEKLFKLLEGLQGPIEVKK*FFESIIKEATRFMRRDLIQHLEKKLEQMI

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	0.21 RPM	0.00 RPM
SRP007412_cerebellum	0.04 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.03 RPM
SRP007412_kidney	0.13 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	0.00 RPM
SRP007412_testis	0.21 RPM	0.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2285 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2285 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3362
Pongo abelii	retro_pabe_2766
Macaca mulatta	retro_mmul_2100
Callithrix jacchus	retro_cjac_1827

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014436	2 retrocopies	retro_cfam_441, retro_cfam_444,
Callithrix jacchus	ENSCJAG00000004135	1 retrocopy	retro_cjac_1827,
Dipodomys ordii	ENSDORG00000008443	1 retrocopy	retro_dord_354,
Homo sapiens	ENSG00000242284	1 retrocopy	retro_hsap_3362,
Macaca mulatta	ENSMMUG00000021984	1 retrocopy	retro_mmul_2100,
Nomascus leucogenys	ENSNLEG00000002303	1 retrocopy	retro_nleu_961,
Pongo abelii	ENSPPYG00000020755	1 retrocopy	retro_pabe_2766,
Pan troglodytes	ENSPTRG00000005890	1 retrocopy	retro_ptro_2164,
Pan troglodytes	ENSPTRG00000041730	1 retrocopy	retro_ptro_2285 ,