RetrogeneDB ID: retro_ptro_2410

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:1480992..1482028(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELF2
• Ensembl ID: ENSPTRG00000016449
• Aliases: None
• Description: None

Sequence

>retro_ptro_2410
ACTCCAGAATTTATCCATGCTGCTATGAGGCCAGATGTCATTACAGAAACTACAGTGGAGGCGTCAACTAAAGAGTCTGA
ACCAATGGATACCTCTCCTATTCCTACATCACCAGATAGCTGTGAACCAAGGAAAAAGAAAACAGTTGGCCATAAACCAA
AGACCCAGCAATCACCAATTTCCAGTGGATCTCCTGAGTTAGGTATAAAGAAACTGAGAGAAGGAAAAGGAAACACAACC
TATTTGTGGGAGTTTCTTTTAGATCTACTTCAAGATAAAAATACTTGTCCCCCGTATATTAAATGGCCTCAGAGAGAAAA
AGGCATATTCAAGCTGGTGGATTCAAAAGCTGTCTCTAAGCTTTGGGGAAAGCATAAGAACAAACCAGACGTGAACGCTG
AAACCATGGGACGAGCTTTGAGATACTATTACCAAAGGGGAATTCTTGCAAAGATTGAAGGACAGAGGCTTGTATATCAG
TTCAAGGATATGCCGAAAAACATAGTGGTCATAGACGATAAAAAAGTGAAACCTGTAATGAAGACTTAGCAGGAGCTATG
GATGAAAAATTATTAGAACAATGTCACTGTCTGCAGAAAGTCTCCTGAAAGCAGCATCCTCTGTTCATGGTGGAAGAAAT
TCATCCCCTATAAACTGCTCCAGAGCAGAGAAGGGTGTGGCTAGATTTGTGAGTATCACTTCCCCTGGTCATGATGCTTC
ATCCAGGTCTCCTATCACTGCATCTGTATCAGCAACAGCAGCTCCAAGGACAGTTCATGTGGCAATGCAAGTACCTGTTG
TAATGACGTCATTGGGCCAGAAAATTTCAGCTGTGGCAGTTCAGTCAAATAATGCAGGTGCACCATTAATAATCAGCACT
AGTACAACAACAGCCACCTCTCCAAAGGCAGTCATTCAGGCAATCCCTACTGTGATGCCAGCTTCTACCGAAAACGGAAA
CAAAATCACCATGCAGTGTCCCCAAATTATTTCCATCCCAGCTACACAGCTCGCTCAGTGTCAACTGCAAAGTCAA

Alignment

ORF - retro_ptro_2410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.14 %
• Parental protein coverage: 59.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPEFIHAAMRPDVITETVVEVSTEESEPMDTSPIPTSPDSHEPMKKKKVGRKPKTQQSPISNGSPELGIK
          .PEFIHAAMRPDVITET.VE.ST.ESEPMDTSPIPTSPDS.EP.KKK.VG.KPKTQQSPIS.GSPELGIK
Retrocopy TPEFIHAAMRPDVITETTVEASTKESEPMDTSPIPTSPDSCEPRKKKTVGHKPKTQQSPISSGSPELGIK

Parental  KKPREGKGNTTYLWEFLLDLLQDKNTCPRYIKWTQREKGIFKLVDSKAVSKLWGKHKNKPDMNYETMGRA
          K..REGKGNTTYLWEFLLDLLQDKNTCP.YIKW.QREKGIFKLVDSKAVSKLWGKHKNKPD.N.ETMGRA
Retrocopy KL-REGKGNTTYLWEFLLDLLQDKNTCPPYIKWPQREKGIFKLVDSKAVSKLWGKHKNKPDVNAETMGRA

Parental  LRYYYQRGILAKVEGQRLVYQFKDMPKNIVVIDDD-KSETCNEDLAGTTDEKSLER-VSLSAESLLKAAS
          LRYYYQRGILAK.EGQRLVYQFKDMPKNIVVIDD..KSETCNEDLAG..DEK.LE...SLSAESLLKAAS
Retrocopy LRYYYQRGILAKIEGQRLVYQFKDMPKNIVVIDDK<KSETCNEDLAGAMDEKLLEQ<MSLSAESLLKAAS

Parental  SVRSGKNSSPINCSRAEKGVARVVNITSPGHDASSRSPTTTASVSATAAPRTVRVAMQVPVVMTSLGQKI
          SV..G.NSSPINCSRAEKGVAR.V.ITSPGHDASSRSP..TASVSATAAPRTV.VAMQVPVVMTSLGQKI
Retrocopy SVHGGRNSSPINCSRAEKGVARFVSITSPGHDASSRSP-ITASVSATAAPRTVHVAMQVPVVMTSLGQKI

Parental  STVAVQSVNAGAPLITSTSPTTATSPKVVIQTIPTVMPASTENGDKITMQPAKIITIPATQLAQCQLQTK
          S.VAVQS.NAGAPLI.STS.TTATSPK.VIQ.IPTVMPASTENG.KITMQ...II.IPATQLAQCQLQ..
Retrocopy SAVAVQSNNAGAPLIISTSTTTATSPKAVIQAIPTVMPASTENGNKITMQCPQIISIPATQLAQCQLQSQ

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	0.13 RPM	14.07 RPM
SRP007412_cerebellum	0.11 RPM	16.92 RPM
SRP007412_heart	0.00 RPM	17.75 RPM
SRP007412_kidney	0.21 RPM	22.83 RPM
SRP007412_liver	0.00 RPM	9.30 RPM
SRP007412_testis	0.00 RPM	93.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2410 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2410 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2410 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3546

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003174	1 retrocopy	retro_cjac_540,
Homo sapiens	ENSG00000109381	1 retrocopy	retro_hsap_3546,
Macaca mulatta	ENSMMUG00000004984	1 retrocopy	retro_mmul_1813,
Pongo abelii	ENSPPYG00000015068	1 retrocopy	retro_pabe_2929,
Pan troglodytes	ENSPTRG00000016449	1 retrocopy	retro_ptro_2410 ,