RetrogeneDB ID: retro_ptro_389

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:206601420..206602099(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUCKS1
• Ensembl ID: ENSPTRG00000001904
• Aliases: None
• Description: None

Sequence

>retro_ptro_389
ATGTCGCGACTCTTCAGAACTAGGAAGGTTTGTTGATTACTCACAGTTTCAGGAATCTGGTGATGCAAATGAAGATTATG
GAAGAGATTCGGGCCCTATCACTAAGAAAATTTCATCATCTCCCCTAGAAGCTAAAAATAAGGCAATCTGGAAAGAATTC
ACAGGAAGATAGTGAGGACTCAGAAGAAAAAGATCTGAAGACAAAGAAGGATGATTTTCACTGAGCAGAGGATAATGAAG
ATGAAAATGAAGTTCATAAAAATGTACGCCAGCACAGCAGGCAGCATCTAAAGCAGCTTCCAAACAGAGCTCATGGGAGA
TGTGGGCATGAGGAAGAACAAGAAGAGGATGAGGCACCCTTCCAGGAGAATTCCAGCAGCAATGAAGATTTCCTGACGGA
AGATGATGACAGTAGTGACTATGGCAATTCAAAAAAGAAAAACAAAAAGATGGTTAAGAAGTCCAAACCTGAGAGAAAAG
AAAAGAAAATGTCCAAACCCAGGCTAAAGGCTACAGTGACGCCAAGTCCAGTGAAAGGCAAAGGGAATGTGGGTCGCCCC
ACAGCTTCAAAGCCATCGAAGGAAAAGATTACTTCTCCCAAGGAAGATGAGGTACCAGAAAGCCCGCCAGAAAAGAAAAC
ATCTACAAGCCCTCACCCAAGAAATCTGGTGATGAAGGC

Alignment

ORF - retro_ptro_389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.53 %
• Parental protein coverage: 95.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSRPVRNRKV-VDYSQFQESDDADEDYGRDSGPPT-KKIRSSPREAKNKRRSGKNSQEDSEDSEDKDVKT
          MSR..R.RKV.VDYSQFQES.DA.EDYGRDSGP.T..K....P...K..R.SGKNSQEDSEDSE.KD.KT
Retrocopy MSRLFRTRKV>VDYSQFQESGDANEDYGRDSGPIT>RKFHHLP*KLKI-RQSGKNSQEDSEDSEEKDLKT

Parental  KKDDSHSAEDSEDEKEDHKNVRQQRQAASKAASKQREMLMEDVGSEEEQEEEDEAPFQEKDSGSDEDFLM
          KKDD.H.AED.....ED...V.......S....KQ...........EE..EEDEAPFQE..S.S.EDFL.
Retrocopy KKDDFH*AEDN----EDENEVHKNVRQHSRQHLKQLPNRAHGRCGHEEEQEEDEAPFQE-NSSSNEDFLT

Parental  EDDDDSDYGSSKKKNKKMVKKSKPERKEKKMPKPRLKATVTPSPVKGKGKVGRPTASKASKEKTPSPKEE
          EDDD.SDYG........MVKKSKPERKEKKM.KPRLKATVTPSPVKGKG.VGRPTASK.SKEK..SPK.E
Retrocopy EDDDSSDYGNXXXXXXXMVKKSKPERKEKKMSKPRLKATVTPSPVKGKGNVGRPTASKPSKEKITSPK-E

Parental  DEEPESPPEKKTSTS-PPPEKSGDEG
          DE.PESPPEKKTSTS.P.P.KSGDEG
Retrocopy DEVPESPPEKKTSTS<PSPKKSGDEG

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	220.27 RPM
SRP007412_cerebellum	0.04 RPM	300.16 RPM
SRP007412_heart	0.00 RPM	215.27 RPM
SRP007412_kidney	0.00 RPM	187.17 RPM
SRP007412_liver	0.00 RPM	130.02 RPM
SRP007412_testis	0.00 RPM	84.10 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_389 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_389 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_521
Gorilla gorilla	retro_ggor_480
Macaca mulatta	retro_mmul_422

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012950	1 retrocopy	retro_amel_339,
Bos taurus	ENSBTAG00000008001	1 retrocopy	retro_btau_541,
Choloepus hoffmanni	ENSCHOG00000001855	1 retrocopy	retro_chof_437,
Dasypus novemcinctus	ENSDNOG00000017212	2 retrocopies	retro_dnov_348, retro_dnov_6,
Dipodomys ordii	ENSDORG00000003183	1 retrocopy	retro_dord_688,
Homo sapiens	ENSG00000069275	1 retrocopy	retro_hsap_521,
Gorilla gorilla	ENSGGOG00000026655	1 retrocopy	retro_ggor_480,
Macropus eugenii	ENSMEUG00000007829	2 retrocopies	retro_meug_2015, retro_meug_372,
Macaca mulatta	ENSMMUG00000005645	1 retrocopy	retro_mmul_422,
Monodelphis domestica	ENSMODG00000001832	1 retrocopy	retro_mdom_980,
Nomascus leucogenys	ENSNLEG00000014564	1 retrocopy	retro_nleu_2576,
Pan troglodytes	ENSPTRG00000001904	1 retrocopy	retro_ptro_389 ,
Rattus norvegicus	ENSRNOG00000047287	2 retrocopies	retro_rnor_2337, retro_rnor_2338,
Tupaia belangeri	ENSTBEG00000015641	1 retrocopy	retro_tbel_2591,
Tarsius syrichta	ENSTSYG00000000910	1 retrocopy	retro_tsyr_987,
Vicugna pacos	ENSVPAG00000003751	1 retrocopy	retro_vpac_313,