RetrogeneDB ID: retro_ptro_2360

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:73303765..73304935(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KNOP1
• Ensembl ID: ENSPTRG00000007836
• Aliases: None
• Description: lysine-rich nucleolar protein 1 [Source:HGNC Symbol;Acc:34404]

Sequence

>retro_ptro_2360
ATGATCACCAAGACACACAAAGCAGACCTGGGCCCTGGGCTCCCAGAGAAGAAAAAGAAGAAGAAAGTGGTCAAAGAACC
AGAGACTCAATACTCAATTTTAAACAATGATGATTACTTTGCCAATGTTTCTCCTATAAGAGCCACATCCCCCTCTAAGA
GTGTGGTCCATGGGAAGGCACCTGAGATGCCTCTAGTGAAGAAAACAAGTAAAAGAAGGGTGTCAGCACCCTTTGCGAGG
AGCACGTAGAACCTGACACCACGCTGCGTGCCAGACGGTCAGAGAAGTCACCCAATCCCAGGAAGCAGGTGCTTGGCCAT
TTGGAGTTCCTCTGTGGGGAGAAGAAAAAGAAGAAGTCACCTCCAGCCATGTCCCATGCCTCTGGGGTGAAAACCTCCCC
AGACCCCAGACAGGGTGAAGAGGAAACCAGAGTTGGCAAGAAGCTCAAATAACACAAGAAGGAAACAAAGCGGGCCCAGG
ACCCCACAGCCCTCTCAGTCCAGAACCCTTGGTTCTGCGAGGCTGGGGATGCTGCGGACACTTGCTCAGTGGGGAAGAAG
GGTGAGGAACAGGCAGCCTTGGGGCAGATAACGGAAGCAGAAAAGCCCCAGGGAGCACAGTGGGAAGGTGAAGAAGAAGA
AAACAAAAATCCACCAGGAGGGAGATGCCCTCCCAGGCCACTCCAAGCCCTTCAGGTCCATGGAGAGCAGCCCTAGGAAA
GGAAGTAAAAAGAAGCCAAAGTTGAGGCTCCGGAATACATCCATCCCCAAAGGAGATGGCCCTAAGGCCCCCGAGAAGAA
AAAGATGAAGTCCAAGAAGGTAGAGCAGCCAATCATTGAGGAGCCGGCTCTGAAAAGGAAGAAAAAGAACAAGAGGAAAG
AGAGTGGGACAGCAAGAGACCCTTGGAAGGAGGAAACAGACACGGACTTAGAGGTGGTGTTGGAAAAGAAAGGCAACATG
GACGAGGCGCACATAGACCAGGTGAGGCGAAAGGCCTTGCAAGGAGAGATCGATCCAGAGTCAGGCAAAACGGAAGCTTC
TGAAACCAGGAAGTGGACGGGAACCTAGTTTGGCCAGTGGGATACTGCTGGTTTTGACAACGAGGAACAGAAACTGAAGT
TTCTCAAACTTACTGGTGGCTTCAAAAACCTGTCCCCTTCGTTCAGCCGC

Alignment

ORF - retro_ptro_2360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.86 %
• Parental protein coverage: 85.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MITKTHKVD--PGLPEKKKKKKVVKEPETRYSVLNNDDYFADVSPLRATSPSKSVAHGQAPEMPLVKKKK
          MITKTHK.D..PGLPEKKKKKKVVKEPET.YS.LNNDDYFA.VSP.RATSPSKSV.HG.APEMPLV.KK.
Retrocopy MITKTHKADLGPGLPEKKKKKKVVKEPETQYSILNNDDYFANVSPIRATSPSKSVVHGKAPEMPLV-KKT

Parental  KK-KKGVSTLCEEHVEPETTLPARRTEKSPSLRKQVLGHLEFLSGEKKNKKSPLAMSHASGVKTSPDPRQ
          .K.KKGVSTLCEEHVEP.TTL.ARR.EKSP..RKQVLGHLEFL.GEKK.KKSP.AMSHASGVKTSPDPRQ
Retrocopy SK<KKGVSTLCEEHVEPDTTLRARRSEKSPNPRKQVLGHLEFLCGEKKKKKSPPAMSHASGVKTSPDPRQ

Parental  GEEETRVGKKLKKHKKEKKGAQDPTAFSVQDPWFCETREARDVGDTCSVGKKDEEQAALGQK-RKRKSPR
          GEEETRVGKKLK.HKKE.K.AQDPTA.SVQ.PWFCE...A.D..DTCSVGKK.EEQAALGQ..RK.KSPR
Retrocopy GEEETRVGKKLK*HKKETKRAQDPTALSVQNPWFCE---AGDAADTCSVGKKGEEQAALGQI>RKQKSPR

Parental  EHNGKMKKKK-KIHQEGDALPGHSKPSRSMESSPRKGSKKKPVKVEAPKYISICDDPKLSAKKKMKSKKN
          EH.GK.KKKK.KIHQEGDALPGHSKP.RSMESSPRKGSKKKP........I...D.PK...KKKMKSKK.
Retrocopy EHSGKVKKKKTKIHQEGDALPGHSKPFRSMESSPRKGSKKKPKLRLRNTSIPKGDGPKAPEKKKMKSKK-

Parental  VEQPVIEEPALKGRK--EKEESGVA-DSWK-ETDTDLEVVLEKKGNMDEAHIDQVRRKA-QEEIDRESGK
          VEQP.IEEPALK..K.....ESG.A.D.WK.ETDTDLEVVLEKKGNMDEAHIDQVRRKA.Q.EID.ESGK
Retrocopy VEQPIIEEPALKRKKKNKRKESGTARDPWKEETDTDLEVVLEKKGNMDEAHIDQVRRKALQGEIDPESGK

Parental  TEASETRKWTGTQFGQWDTAGFENEDQKLKFLRLMGGFKNLSPSFSR
          TEASETRKWTGT.FGQWDTAGF.NE.QKLKFL.L.GGFKNLSPSFSR
Retrocopy TEASETRKWTGT*FGQWDTAGFDNEEQKLKFLKLTGGFKNLSPSFSR

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	0.18 RPM	3.83 RPM
SRP007412_cerebellum	0.00 RPM	4.34 RPM
SRP007412_heart	0.00 RPM	2.07 RPM
SRP007412_kidney	0.00 RPM	4.03 RPM
SRP007412_liver	0.00 RPM	3.83 RPM
SRP007412_testis	0.21 RPM	4.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2360 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2360 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3487
Macaca mulatta	retro_mmul_1771

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018032	2 retrocopies	retro_cfam_1557, retro_cfam_1763,
Callithrix jacchus	ENSCJAG00000009625	1 retrocopy	retro_cjac_3199,
Homo sapiens	ENSG00000103550	3 retrocopies	retro_hsap_3487, retro_hsap_4007, retro_hsap_979,
Gorilla gorilla	ENSGGOG00000005673	1 retrocopy	retro_ggor_2691,
Macaca mulatta	ENSMMUG00000002707	2 retrocopies	retro_mmul_1771, retro_mmul_798,
Nomascus leucogenys	ENSNLEG00000012496	2 retrocopies	retro_nleu_1618, retro_nleu_551,
Otolemur garnettii	ENSOGAG00000010065	4 retrocopies	retro_ogar_1115, retro_ogar_1480, retro_ogar_1481, retro_ogar_2259,
Pongo abelii	ENSPPYG00000007151	3 retrocopies	retro_pabe_3293, retro_pabe_828, retro_pabe_920,
Pan troglodytes	ENSPTRG00000007836	3 retrocopies	retro_ptro_2360 , retro_ptro_767, retro_ptro_924,