RetrogeneDB ID: retro_pabe_999

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:47898684..47899721(+)
• 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_999
ATGGCAGACATTGACAACAAAGAACAGTCTGAACTTGATCAAGATTTGGATGACGCTGAAAAAGTAGAAGAAGAAACAAA
AATCAAAGCACATCAGCTAACTGTTCAGATGATGCAAAATCCTCAGATTCTTGCAGCCTTTCAAGAAAGACTTGGTGGTC
TAATAGAAACCCCAACAGGATACATTGAAAGCCTGCCTAGAGTAGTTAAAAAACGAGTGAATGCTCTCAAAAACCTGTAA
GTTAAATGTGCACAGATAGAAGCCAAATTCTATGAGGAAGTTCACAATCTTGAAAGGAAGTATGCTGTTCTCTGTCAGCC
TCTATTTGATAAGCAATTTGAGATTATTAATGCAATTACGAACCTACAGAAGAAGAATGGAAACCAGATGAAGAAGATGA
GATCTCAGAGGAGTTGAAATAAAAGGCCATGATTGAAGATAAGAAAAAAGATGAAGAAAAAGAAGATTCCAAAGGAATTC
CTGAATTTTGGTTAACTTTTTAAGAATGTTGACTTGCTCAGTGATATGCTTCAGGAACATGATGAACCTATTCTGAAGCA
CTTGAAAGATATTAAAGTGAAGTTCTCAGATGCTGGCCAGCCCATGAGTTTTGTCTTAGAATTTCACTTTGAAGCCAATG
AATATTTTACAAATGAAGTGCTGACAAAGACGTATAGCATGAGGTCAGAACCAGATGATTCTGATCCCTTTTATTTTGAT
GGACCAGAAATTATGGGTTTTACAGGATGCCAGATAGATTGGAAAAAAGGAAAGAATGTCACCTTGAAAACCATTAAGAA
GAAGCAGAAATACAAGGGACGTGGGACAGTTAGTTCTGTGGATTAAAACAGTTTCCAATGACTCTTTCTTTAAATTTTTT
GCCCCTCCTGAAGTTTCTGAGAGCGGAGATCTGGATGATGACGCTAAAACAATCCTTGCTGCAGACTTCAAAACTGGTCA
CTTTTTACCTGAACATATAATCTCAGGATCAGTGTTATACTTTACTGGAGAAGCTATTGAAGATGGATGATGATGAT

Alignment

ORF - retro_pabe_999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 90.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MADIDNKEQSELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
          MADIDNKEQSELDQ...D....E..E..EETKIKA.QLTVQMMQNPQILAA.QERL.GL.ETPTGYIESL
Retrocopy MADIDNKEQSELDQ---DLDDAEKVE--EETKIKAHQLTVQMMQNPQILAAFQERLGGLIETPTGYIESL

Parental  PRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAI-YEPTEEECEWKPDEE
          PRVVK.RVNALKNL.VKCAQIEAKFYEEVH.LERKYAVL.QPLFDK.FEIINAI.YEPTEEE..WKPDEE
Retrocopy PRVVKKRVNALKNL*VKCAQIEAKFYEEVHNLERKYAVLCQPLFDKQFEIINAI<YEPTEEE--WKPDEE

Parental  DEISEELKEKAKIEDEKKDEE-KEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQ
          DEISEELK.KA.IED.KKDEE.K..PK....F....FKNVDLLSDM.QEHDEPILKHLKDIKVKFSDAGQ
Retrocopy DEISEELK*KAMIEDKKKDEE>KKIPKEFLNFG*-LFKNVDLLSDMLQEHDEPILKHLKDIKVKFSDAGQ

Parental  PMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQK
          PMSFVLEFHFE.NEYFTNEVLTKTY.MRSEPDDSDPF.FDGPEIMG.TGCQIDWKKGKNVTLKTIKKKQK
Retrocopy PMSFVLEFHFEANEYFTNEVLTKTYSMRSEPDDSDPFYFDGPEIMGFTGCQIDWKKGKNVTLKTIKKKQK

Parental  HKGRGTVRTV-TKTVSNDSFFNFFAPPEVPESGDLDDDAEAILAADFEIGHFLRERIIPRSVLYFTGEAI
          .KGRGTV..V..KTVSNDSFF.FFAPPEV.ESGDLDDDA..ILAADF..GHFL.E.II..SVLYFTGEAI
Retrocopy YKGRGTVSSV>IKTVSNDSFFKFFAPPEVSESGDLDDDAKTILAADFKTGHFLPEHIISGSVLYFTGEAI

Parental  ED-DDDD
          ED.DDDD
Retrocopy ED>DDDD

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

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_999 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_999 has 0 orthologous retrocopies within eutheria group .

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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,