RetrogeneDB ID: retro_ptro_808

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:23883394..23883943(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUS1
• Ensembl ID: ENSPTRG00000018547
• Aliases: None
• Description: None

Sequence

>retro_ptro_808
GCTGCTGCCGCGCCGCCTCTGCCGCGGTCCTAGAGCCGCTTGGCTTCACGCTCCGCAAGCAGGAACAGACCTCACCACAC
GCACCCGCGCGGGGGGGAGTGCCTGCCCGCAGCCCCCCACCGAATGCGCTGGCGCGCGGACGGCCCTTCCCTGGAGAAGC
TGCCTGTGCACATGGGCCTGGTGATCACCGAGATGGAGCAGGAACCCAGCTTCTCGGACATCGCGAGCCTCGTGGTGTGG
TGTATGGCCGTGGGCATCTTCTACATTAGCATCTACGACCACCAAGGTATTTTCAAAAGAAATAATTCCAGATTGATGGA
TGGAATTTTAAAACAACAGCAAGAACTTCTGGGCCTAGATTGTTCAAAATACTCACCAGAGTTTGCAAATAGTAACGACA
AAGACGATCAAGTTTTAAATTGCCATTTGGCAGTGAAGGTGCTATCCCCGGAAGATGGAAAAGCAGATATTGTGAGAGCT
GCTCAGGACTTTTGCCAGTGAGTAGCCCAGAAGCAAAGGAGACCCACAGATTTGGATGTAGATATGTTA

Alignment

ORF - retro_ptro_808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.15 %
• Parental protein coverage: 62.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASAAVLAPLGFTLRKSPAVGRNRRHHRHPRGGSCLAAAHHRMRWRADGRSLEKLPVHMGLVITEVEQEPS
          A.AA...P.......S....RNR.HH.HPRGG.CL.AA.HRMRWRADG.SLEKLPVHMGLVITE.EQEPS
Retrocopy AAAAPPLPRS*SRLASRSASRNRPHHTHPRGGECLPAAPHRMRWRADGPSLEKLPVHMGLVITEMEQEPS

Parental  FSDIASLVVWCMAVGISYISVYDHQGIFKRNNSRLMDEILKQQQELLGLDCSKYSPEFANSNDKDDQVSN
          FSDIASLVVWCMAVGI.YIS.YDHQGIFKRNNSRLMD.ILKQQQELLGLDCSKYSPEFANSNDKDDQV.N
Retrocopy FSDIASLVVWCMAVGIFYISIYDHQGIFKRNNSRLMDGILKQQQELLGLDCSKYSPEFANSNDKDDQVLN

Parental  CHLAVKVLSPEDGKADIVRAAQDFCQLVAQKQKRPTDLDVDTL
          CHLAVKVLSPEDGKADIVRAAQDFCQ.VAQKQ.RPTDLDVD.L
Retrocopy CHLAVKVLSPEDGKADIVRAAQDFCQ*VAQKQRRPTDLDVDML

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	18.82 RPM
SRP007412_cerebellum	0.00 RPM	8.17 RPM
SRP007412_heart	0.00 RPM	6.73 RPM
SRP007412_kidney	0.00 RPM	19.56 RPM
SRP007412_liver	0.00 RPM	11.46 RPM
SRP007412_testis	0.00 RPM	5.90 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_808 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_808 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_808 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1176

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001780	1 retrocopy	retro_dnov_1639,
Erinaceus europaeus	ENSEEUG00000008948	1 retrocopy	retro_eeur_443,
Homo sapiens	ENSG00000153989	4 retrocopies	retro_hsap_1174, retro_hsap_1176, retro_hsap_1289, retro_hsap_4825,
Gorilla gorilla	ENSGGOG00000022321	4 retrocopies	retro_ggor_1012, retro_ggor_914, retro_ggor_915, retro_ggor_993,
Microcebus murinus	ENSMICG00000007831	1 retrocopy	retro_mmur_423,
Nomascus leucogenys	ENSNLEG00000013457	1 retrocopy	retro_nleu_2411,
Oryctolagus cuniculus	ENSOCUG00000011553	1 retrocopy	retro_ocun_1713,
Pongo abelii	ENSPPYG00000025886	1 retrocopy	retro_pabe_81,
Pan troglodytes	ENSPTRG00000018547	1 retrocopy	retro_ptro_808 ,
Tarsius syrichta	ENSTSYG00000003212	1 retrocopy	retro_tsyr_633,
Tursiops truncatus	ENSTTRG00000007352	2 retrocopies	retro_ttru_358, retro_ttru_684,