RetrogeneDB ID: retro_pabe_2287

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:11840300..11841155(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSPPYG00000004786
• Aliases: None
• Description: nucleosome assembly protein 1-like 1 [Source:RefSeq peptide;Acc:NP_001126986]

Sequence

>retro_pabe_2287
TATGCTGTTCTCTATCAGCCTCTATTTGATAAGCGATTTGAGATTATTAATGCAATTTATGAACCTACGGAAGAAGAATG
CGGATGGAAACCAGATGAAGAAGACGAGATTTCGGAGGAGTTGAAAGAAAAGGCCAAGATTGAAGAAGAGAAGAAGGATG
AAGAAAAAGAAGAGCCCATAGGAATTCCTGAATTTTGGTTAACTATTTTTAAGAGTGTTGACTTGCTTAGTGATATGCTT
CAGGAACATGATGAACCTATTCTGAAGCACTTGAAATATATTAAAGTGAAGTTCTTGGATGCTGGCCAGCCTATGAGTTT
TGTCTTAGAATTTCACTTTGAACCCAGTGAATATTTTACAAATGAAGTGCCAACAAAGACATATAGGATGAGGTCAGAAC
CAGATGATTCTGATCCCTTTTCTTTTGATGGACTAGAAATTATGGGTTGTAAAGGGTGCCAGATAGATTGGAAAAAAAGA
AAGGATGTCACTTTGAGAAACATTAAGAAGAAGCAGAAACACAAGGGACATGGGACAGTTTGTACTGTGACTAAAACAGT
TTCCAATGACTCTTGCTTTAATTTTTTTGCCCCTCCTGAAGTTCCTGAGAGTGGAGATCTGGATGATGCTGCTGAAGCTA
TCCATGCTGCAAACTTCCAAATCGGTCACTTTTTACCTGAGCATATAATCCCAAGATCAGTGTTATATTTTACTGGAGAA
GATATTGAAGATGATGATGATTATTATGATGAAGAAGGCAAAGAAGCAGATGAGGAAGGGGAAGAAGAAGATGAGGAAAA
TGATCCAGACTATGAACCAAAGAAAGATCAAAACCCAGCGGAGTGCAAGCAGCAG

Alignment

ORF - retro_pabe_2287 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 73.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEEDEISEELKEKAKIEDEKKDEEKEDPKGIPEFWLTVF
          YAVLYQPLFDKRFEIINAIYEPTEEEC.WKPDEEDEISEE..................P.GIPEFWLT.F
Retrocopy YAVLYQPLFDKRFEIINAIYEPTEEECGWKPDEEDEISEEXXXXXXXXXXXXXXXXXXPIGIPEFWLTIF

Parental  KNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPF
          K.VDLLSDM.QEHDEPILKHLK.IKVKF.DAGQPMSFVLEFHFEP.EYFTNEV.TKTYRMRSEPDDSDPF
Retrocopy KSVDLLSDMLQEHDEPILKHLKYIKVKFLDAGQPMSFVLEFHFEPSEYFTNEVPTKTYRMRSEPDDSDPF

Parental  SFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQKHKGRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDD
          SFDG.EIMGC.GCQIDWKK.K.VTL..IKKKQKHKG.GTV.TVTKTVSNDS.FNFFAPPEVPESGDLDD.
Retrocopy SFDGLEIMGCKGCQIDWKKRKDVTLRNIKKKQKHKGHGTVCTVTKTVSNDSCFNFFAPPEVPESGDLDDA

Parental  AEAILAADFEIGHFLRERIIPRSVLYFTGEAIEDDDDDYDEEGEEADEEGEEEGDEENDPDYDPKKDQNP
          AEAI.AA.F.IGHFL.E.IIPRSVLYFTGE.IEDDD.DY..................NDPDY.PKKDQNP
Retrocopy AEAIHAANFQIGHFLPEHIIPRSVLYFTGEDIEDDD-DYYXXXXXXXXXXXXXXXXXNDPDYEPKKDQNP

Parental  AECKQQ
          AECKQQ
Retrocopy AECKQQ

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	163.33 RPM
SRP007412_cerebellum	0.12 RPM	115.52 RPM
SRP007412_heart	0.00 RPM	91.70 RPM
SRP007412_kidney	0.03 RPM	113.56 RPM
SRP007412_liver	0.00 RPM	66.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2287 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2287 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2696
Pan troglodytes	retro_ptro_1820
Gorilla gorilla	retro_ggor_1879

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Choloepus hoffmanni	ENSCHOG00000003210	2 retrocopies	retro_chof_1095, retro_chof_2057,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Pongo abelii	ENSPPYG00000002938	1 retrocopy	retro_pabe_288,
Pongo abelii	ENSPPYG00000004786	2 retrocopies	retro_pabe_2287 , retro_pabe_999,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,