RetrogeneDB ID: retro_ptro_549

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:70006932..70007292(+)
• Located in intron of: ENSPTRG00000004032

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2AF1
• Ensembl ID: ENSPTRG00000013952
• Aliases: None
• Description: None

Sequence

>retro_ptro_549
TTTCACCGTGAGGAAGATGTGGAAAAGGCTGTGATTGACTTGTATAACCGTTGGTTTAACGGACAGCCAATCCACACCGA
GCTGTCGCCTGTGACCGACTTCAGAGAAGCCTGCTGCAGTCAGTATGAGATGGGAGAATGCACACGAGGCGGCTTCTGCA
ACTTCATGCATTTGAAGCCCATTTCCAGAGAGCTGAGGCGGGAGCTGTATGGGTGCCATCCCAAGAAGCATAGATCAAGA
TCCCAGTCCCGGGAGTGTAGTTCTCAGTCTAGAGACCATGGTGGTGGCGGTGGTGGAGGCGGCGGCAGGCGGGAGTGTGA
CAGGAGGCGGTTGAGAGATCATGAAAGATCTGGGCAATTC

Alignment

ORF - retro_ptro_549 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.26 %
• Parental protein coverage: 51.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FRREEDAEKAVIDLNNRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRRELY
          F.REED.EKAVIDL.NRWFNGQPIH.ELSPVTDFREACC.QYEMGECTRGGFCNFMHLKPISRELRRELY
Retrocopy FHREEDVEKAVIDLYNRWFNGQPIHTELSPVTDFREACCSQYEMGECTRGGFCNFMHLKPISRELRRELY

Parental  GRRRKKHRSRSRSRERRSRSRDRGRGGGGGGGGGGGGRERDRRRSRDRERSGRF
          G...KKHRSRS.SRE..S.SRD.G....GGGGGGGG.RE.DRRR.RD.ERSG.F
Retrocopy GCHPKKHRSRSQSRECSSQSRDHG----GGGGGGGGRRECDRRRLRDHERSGQF

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	0.02 RPM	30.92 RPM
SRP007412_cerebellum	0.04 RPM	72.49 RPM
SRP007412_heart	0.00 RPM	31.59 RPM
SRP007412_kidney	0.00 RPM	52.46 RPM
SRP007412_liver	0.00 RPM	83.34 RPM
SRP007412_testis	0.21 RPM	79.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_549 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_549 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_790
Pongo abelii	retro_pabe_703
Macaca mulatta	retro_mmul_1071

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013835	1 retrocopy	retro_mmur_614,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pan troglodytes	ENSPTRG00000013952	2 retrocopies	retro_ptro_1000, retro_ptro_549 ,
Pan troglodytes	ENSPTRG00000021693	1 retrocopy	retro_ptro_25,
Tupaia belangeri	ENSTBEG00000000453	2 retrocopies	retro_tbel_2115, retro_tbel_963,
Vicugna pacos	ENSVPAG00000002856	1 retrocopy	retro_vpac_489,