RetrogeneDB ID: retro_pabe_288

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:111632956..111634076(+)
• Located in intron of: ENSPPYG00000000982

Retrocopy information

• Ensembl ID: ENSPPYG00000000983
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAP1L4
• Ensembl ID: ENSPPYG00000002938
• Aliases: None
• Description: nucleosome assembly protein 1-like 4 [Source:RefSeq peptide;Acc:NP_001125446]

Sequence

>retro_pabe_288
ATGGCAGATAACAGTTTTTCAGATGGGGTTCCTTCAGATTTCGTGGAAGCTGCTAAAAATGCAAGTAAGATGGAAAAGCT
CACGGATCAGGTGATGCAGAATCCTGGAGTTTTGGCAGCTTTACAGGAGCGACTTGACAATGCCCCTCACACCCCTTCCA
GCTACATCGAAACTTTACCTAAAGCAGTAAAAAGAAGAATTAATGCATTGAAACAAATTCAGGTGAGATGCGCTCATATA
GAAGCCAAGTTCTATGAAGAAGTTCATGACTTGAAAAGAAAATATGCAGCATTATACCAGCCTCTCTTTGACAAGAGAAG
AGAATTTATCACCGGTGATGTTGAACCAACATCTGATACGGAATCAGAATGGCACAGTGAAAATGAAGAGGAGGAGAAAT
TGGCTGGAGACATGAAAAATAAAGTAGTCATAACAGAAAAAGTAGCGACAACAGCTGAAGAGCCAAATCCCAAAGGAATT
CCAGAGTTTTGGTTTACCATCTTTAGAAATGTAGATATGCTAAGTGAATTAGTCCAGAAATATGATGAACCAATCTTGAA
ACACCTGCAGGATATTAAAGTGAAGTTTTCTGACCCTGGACAGCCTATGTCTTTCATATTAAGAGTTCCACTTTGAACCC
AACGACTACTTTGCCAACTCAGTCCTGACAAAAACCTGCAAGATGAAATCAGAACCAGATAAGGCTGATCCCTTTTCATT
TGCAGGTCCTGAGATCATGGACTGTGATGGGTGTACTATTGACTGGAAGAAAGGAAAGAATGTTACTGTCAAAACCATCA
AGAAAAAGCAGAAGCATAAGGGTCCAGGCGCTGTTAGAACAATTACCAAGCAAGTATCCATTGAGTCATTTTTCAACTTC
TTCAATCCACTGAAAGCATCTGGGGATAGAGAATCACTGGATAAAGATTCTGAATTCGTATTAGCCTCTGATTTTGAAAC
TGGACACTTTTTCCGTGAGCGGATAGTCCCACAGGCTGTGCTGTACTTCGCTAGGGAGGCCTTAGAGGATGATGACAATT
TTGACGAAGATGAAGAAGAAGAGGACGAATTAGAAGGTGACAAGGAGGGAGAAGATGAGGATGAGGTGGAAATTAATCCC

Alignment

ORF - retro_pabe_288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.8 %
• Parental protein coverage: 99.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADHSFSDGVPSDSVEAAKNASNTEKLTDQVMQNPRVLAALQERLDNVPHTPSSYIETLPKAVKRRINAL
          MAD.SFSDGVPSD.VEAAKNAS..EKLTDQVMQNP.VLAALQERLDN.PHTPSSYIETLPKAVKRRINAL
Retrocopy MADNSFSDGVPSDFVEAAKNASKMEKLTDQVMQNPGVLAALQERLDNAPHTPSSYIETLPKAVKRRINAL

Parental  KQLQVRCAHIEAKFYEEVHDLERKYAALYQPLFDKRREFIT-DVVPT-DAE-EWHSENEEEEKLAGDMKN
          KQ.QVRCAHIEAKFYEEVHDL.RKYAALYQPLFDKRREFIT.DV.PT.D.E.EWHSENEEEEKLAGDMKN
Retrocopy KQIQVRCAHIEAKFYEEVHDLKRKYAALYQPLFDKRREFITGDVEPTSDTESEWHSENEEEEKLAGDMKN

Parental  KVVVTEKEAATAEEPNPKGIPEFWFTIFRNVDMLSELVQEYDEPILKHLQDIKVKFSDPGQPMSFVL-EF
          KVV.TEK.A.TAEEPNPKGIPEFWFTIFRNVDMLSELVQ.YDEPILKHLQDIKVKFSDPGQPMSF.L.EF
Retrocopy KVVITEKVATTAEEPNPKGIPEFWFTIFRNVDMLSELVQKYDEPILKHLQDIKVKFSDPGQPMSFIL>EF

Parental  HFEPNDYFSNSVLTKTYKMKSEPDKADPFSFEGPEIVDCDGCTIDWKKGKNVTVKTIKKKQKHKGRGTVR
          HFEPNDYF.NSVLTKT.KMKSEPDKADPFSF.GPEI.DCDGCTIDWKKGKNVTVKTIKKKQKHKG.G.VR
Retrocopy HFEPNDYFANSVLTKTCKMKSEPDKADPFSFAGPEIMDCDGCTIDWKKGKNVTVKTIKKKQKHKGPGAVR

Parental  TITKQVPNESFFNFFNPLKASGDGESLDEDSEFTLASDFEIGHFFRERIVPRAVLYFTGEAIEDDDNFEE
          TITKQV..ESFFNFFNPLKASGD.ESLD.DSEF.LASDFE.GHFFRERIVP.AVLYF..EA.EDDDNF.E
Retrocopy TITKQVSIESFFNFFNPLKASGDRESLDKDSEFVLASDFETGHFFRERIVPQAVLYFAREALEDDDNFDE

Parental  GEEGEEEELEGDEEGEDEDDAEINP
          .EE.EE.ELEGD.EGEDED..EINP
Retrocopy DEE-EEDELEGDKEGEDEDEVEINP

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	0.44 RPM	99.36 RPM
SRP007412_cerebellum	0.61 RPM	105.55 RPM
SRP007412_heart	0.72 RPM	57.23 RPM
SRP007412_kidney	0.89 RPM	93.11 RPM
SRP007412_liver	0.46 RPM	55.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_288 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_288 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_438
Pan troglodytes	retro_ptro_192
Gorilla gorilla	retro_ggor_423

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 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 ,
Pongo abelii	ENSPPYG00000004786	2 retrocopies	retro_pabe_2287, retro_pabe_999,
Pan troglodytes	ENSPTRG00000028747	1 retrocopy	retro_ptro_192,