RetrogeneDB ID: retro_ptro_192

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:120203170..120203867(+)
• Located in intron of: ENSPTRG00000001153

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L4
• Ensembl ID: ENSPTRG00000028747
• Aliases: None
• Description: None

Sequence

>retro_ptro_192
AGAGAAGTTATCACCGGTGATGTTGAACCAACATCTGATATGGAATCAGAATGGCACCGTGAAAATGAAGAGGAGGAGAA
ATTGGCTGGAGACAGGAAAAATAAAGTAGTCATAACAGAAAAAGCAGCAGCAACAGCTGAAGAGCCAAATCCCAAAGGAA
TTCCAGAGTTCTGGTTTACCATCTTTAGAAATGTAGATATGCTAAGTGAATTAGTCCAGGAATATGATGAACCAATCTTG
AAATACCTGCAGGATATTAAAGTGAAGTTTTCTGACCCTGGACAGCCTATGTCTTTCATATTAAGAGTTCCACTTTCAAC
CCAACGACTGCTTTGCCAACTCAGTCCTGACAAAAACCTGCAAGATGAAATCAGAACCAGATAAGGCTGATCCCTTTTCA
TTTGCAGGTCCTGAGATCATGGACTGCGACGGGTGTACTATTGACTGGAAGAAAGGAAAGAATGTTACTGTCAAAACCAT
CAAGAAGAAGCAGAAGCGTAAGGGTCCAGGCACTGTTAGAACAATTACCAAACAAGTATCCAACGAGTCATTTTTCAACT
TCTTCAATCCACTGAAAGCATCTGGGGACAGAGAATCACTGGATAAAGATTCTGAATTCGTATTAGCCTCTGATTTTGAA
ATTGGACACTTTTTCCGTGAGCGGACTACAGGCTGTGCTGTACTTCGCTGGGGAGGC

Alignment

ORF - retro_ptro_192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.55 %
• Parental protein coverage: 61.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  REFITGDVEPT-DAESEWHSENEEEEKLAGDMKNKVVVTEKEAATAEEPNPKGIPEFWFTIFRNVDMLSE
          RE.ITGDVEPT.D.ESEWH.ENEEEEKLAGD.KNKVV.TEK.AATAEEPNPKGIPEFWFTIFRNVDMLSE
Retrocopy REVITGDVEPTSDMESEWHRENEEEEKLAGDRKNKVVITEKAAATAEEPNPKGIPEFWFTIFRNVDMLSE

Parental  LVQEYDEPILKHLQDIKVKFSDPGQPMSFVL-EFHFEPNDYFTNSVLTKTYKMKSEPDKADPFSFEGPEI
          LVQEYDEPILK.LQDIKVKFSDPGQPMSF.L.EFHF.PND.F.NSVLTKT.KMKSEPDKADPFSF.GPEI
Retrocopy LVQEYDEPILKYLQDIKVKFSDPGQPMSFIL>EFHFQPNDCFANSVLTKTCKMKSEPDKADPFSFAGPEI

Parental  VDCDGCTIDWKKGKNVTVKTIKKKQKHKGRGTVRTITKQVPNESFFNFFNPLKASGDGESLDEDSEFTLA
          .DCDGCTIDWKKGKNVTVKTIKKKQK.KG.GTVRTITKQV.NESFFNFFNPLKASGD.ESLD.DSEF.LA
Retrocopy MDCDGCTIDWKKGKNVTVKTIKKKQKRKGPGTVRTITKQVSNESFFNFFNPLKASGDRESLDKDSEFVLA

Parental  SDFEIGHFFRERIVPRAVLYFTG
          SDFEIGHFFRER....AVL...G
Retrocopy SDFEIGHFFRERTTGCAVLRWGG

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	0.05 RPM	94.95 RPM
SRP007412_cerebellum	0.00 RPM	89.91 RPM
SRP007412_heart	0.26 RPM	80.71 RPM
SRP007412_kidney	0.16 RPM	94.38 RPM
SRP007412_liver	0.03 RPM	64.91 RPM
SRP007412_testis	0.11 RPM	272.21 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_192 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_192 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_438
Gorilla gorilla	retro_ggor_423
Pongo abelii	retro_pabe_288

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000205531	1 retrocopy	retro_hsap_438,
Gorilla gorilla	ENSGGOG00000013223	1 retrocopy	retro_ggor_423,
Nomascus leucogenys	ENSNLEG00000010841	1 retrocopy	retro_nleu_1876,
Oryctolagus cuniculus	ENSOCUG00000005624	1 retrocopy	retro_ocun_384,
Pongo abelii	ENSPPYG00000002938	1 retrocopy	retro_pabe_288,
Pan troglodytes	ENSPTRG00000005240	4 retrocopies	retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Pan troglodytes	ENSPTRG00000028747	1 retrocopy	retro_ptro_192 ,