RetrogeneDB ID: retro_ptro_924

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:59230758..59231788(+)
• 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_924
CATGATGGTTACTTCGCTGATGTTCTCTTAAGAGCTACATCCCCTCTAAGAGTGTGGCCCATGGGCAGGCACCTGAGATG
CCCCTAGTGAAGAAAAAGAAGAAGAAAAAGAAGGGTGTCAGCACCCTTTGCGAGGAGCATGTAGAACCTGAGACCACGCT
GCTTGCCAGACGGACAGAGAAGTCACCCAGCCTCAGGAAGCAGGTGCTTGGCCACTTGGAGTTCCTCAGTGGGGAAAAGA
AAAATAAGAAGTCACCTCTAGCCATGTCCCATGCCTCTGGGGTGAAAACCTCCCCAGACCCTAGACAGGGTGAGGAGGAA
ACCAGAGTTGGCAAGAAGCTCAAAAAGCACAAGAAGGAAAAAAGGGGGCCCAGGACCCCACAGCCTTCTCAGTCCAGGAC
CCTTGGTTCTCTGAGGCCAGGGAGGCCAGGGATGTTGGGGACACTTGCTCAGTGGGGAAGAAGGATGAGGAACAAGCAGC
CTTGGGGCAGAAACGGAAGCGGAAGAGCCCCAGAGAACACAATGGGAAGGTGAAGAAGAAAAAAAAAAAAATCCACCAGG
AGGGAGACGCCCTCCCAGGCCACTCCAAGCCCTCCAGGTCCATGGAGAGCAGCCCTAGGAAAGGAAGTAAAAAGAAGCCA
GTCAAAGTTGAGGCTCCGGAATACATCCCCATAAGTGATGACCCTAAGGCCTCCGCAAAGAAAAAGATGAAGTCCAAAAA
GAAGGTAGAGCAGCCAGTCATCGAGGAGCCAGCTCTGAAAAGGAAGAAAAAGAAGAAGAGGAAAGAGAGTGGCGTAGCAG
GAGACCCTTGGAAGGAGGAAACAGACACAGACTTAGAGGTGGTGTTGGAAAAAAAAGGCAACACGGATGAGGCGCACATA
GACCAGGTGAGGCGAAAGGCCTTGCAAGAAGAGATCGATCGCGAGTCAGGCAGAACGGAAGCTTCTGAAACCAGGAAGTG
GACGGGAACCCAGTTTGGCCAGTGGGATACTGCTGGTTTTGAGAACGAGGACCAGAAACTGAAATTTCTG

Alignment

ORF - retro_ptro_924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.59 %
• Parental protein coverage: 74.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NDDYFADVSPLRATSP-SKSVAHGQAPEMPLVKKKKKKKKGVSTLCEEHVEPETTLPARRTEKSPSLRKQ
          .D.YFADV..LRATSP.SKSVAHGQAPEMPL.........GVSTLCEEHVEPETTL.ARRTEKSPSLRKQ
Retrocopy HDGYFADVL-LRATSP<SKSVAHGQAPEMPLXXXXXXXXXGVSTLCEEHVEPETTLLARRTEKSPSLRKQ

Parental  VLGHLEFLSGEKKNKKSPLAMSHASGVKTSPDPRQGEEETRVGKKLKKHKKEK-KGAQDPTAFSVQDPWF
          VLGHLEFLSGEKKNKKSPLAMSHASGVKTSPDPRQGEEETRVGKKLKKHKKEK.KGAQDPTAFSVQDPWF
Retrocopy VLGHLEFLSGEKKNKKSPLAMSHASGVKTSPDPRQGEEETRVGKKLKKHKKEK<KGAQDPTAFSVQDPWF

Parental  CETREARDVGDTCSVGKKDEEQAALGQKRKRKSPREHNGKMKK-KKKIHQEGDALPGHSKPSRSMESSPR
          ........VGDTCSVGKKDEEQAALGQKRKRKSPREHNGK.KK.....HQEGDALPGHSKPSRSMESSPR
Retrocopy SXXXXXXXVGDTCSVGKKDEEQAALGQKRKRKSPREHNGKVKKXXXXXHQEGDALPGHSKPSRSMESSPR

Parental  KGSKKKPVKVEAPKYISICDDPKLSAKKKMKSKKNVEQPVIEEPALKGRKEK--EESGVA-DSWK-ETDT
          KGSKKKPVKVEAP.YI.I.DDPK.SAKKKMKSKK.VEQPVIEEPALK..K.K...ESGVA.D.WK.ETDT
Retrocopy KGSKKKPVKVEAPEYIPISDDPKASAKKKMKSKKKVEQPVIEEPALKRKKKKKRKESGVAGDPWKEETDT

Parental  DLEVVLEKKGNMDEAHIDQVRRKA-QEEIDRESGKTEASETRKWTGTQFGQWDTAGFENEDQKLKFL
          DLEVVL...GN.DEAHIDQVRRKA.QEEIDRESG.TEASETRKWTGTQFGQWDTAGFENEDQKLKFL
Retrocopy DLEVVLXXXGNTDEAHIDQVRRKALQEEIDRESGRTEASETRKWTGTQFGQWDTAGFENEDQKLKFL

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	0.63 RPM	3.83 RPM
SRP007412_cerebellum	1.79 RPM	4.34 RPM
SRP007412_heart	0.70 RPM	2.07 RPM
SRP007412_kidney	0.86 RPM	4.03 RPM
SRP007412_liver	1.47 RPM	3.83 RPM
SRP007412_testis	1.48 RPM	4.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_924 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_924 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_924 has 0 orthologous retrocopies within eutheria group .

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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 ,