RetrogeneDB ID: retro_pabe_1398

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:57229021..57230429(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NONO
• Ensembl ID: ENSPPYG00000020451
• Aliases: None
• Description: non-POU domain-containing octamer-binding protein [Source:RefSeq peptide;Acc:NP_001124612]

Sequence

>retro_pabe_1398
ATGCACAGTAATAAAACTTTTAACTTGGAGAAGCAAAACCATACTCCAAGAAAGCATCATCAACGTCATCAACGTCACCA
CCAGCAGCAACACCAGCAGCCGCCACCACCGCCAATACCTGCAAATGGGCAACAGGTCAGCAGCCAAAATGAAGGCTTGG
CTATTTGACCTGAAGAATTTTAGAAAACCAGGAGAGAAGACCTTCACCCAATGAAGCCGTCTTTTTGTGGGAAATCTTCC
TCCCGACATCACTGAGGAAGAAATGAGGAAACTATTTAAGAAATATGGAAAGGCAGGCAAAGTCTTCATTCATAAGGATT
AAGGATTTGGCTTTATCCGCTTGGAAACACGAACCCTAGCGGAGATTGCGAAAGTGGAGCTGGACAATAAGCCACTCTGT
GGAAAGCAGCTGTGTGTGCACTTTTCCTGCCATAGTGCATCCCTTACAGTTCGAAACCTTCCTCAGTATGTGTCAAACGA
ACTGCTGGAAGAAGCCTTTTCTGTGTTTGGCCAGGTAGAGAGGGCTGTAGTCATTGTGGGTGATCGAGGAAGGCCCTCAG
GAAAAGGCATTGTTGAGTTCTCAGGGAAGCCAGCTGCTGGGAAAGCTCTGGACAGATGCAGTGAAGGCTCCTTCCTGCTA
ACCACATTTCTTTGTCCTGTGACTATGGAGCCCATGGACCAGTTAGATGATGAAGAGGGACTTCCAGAGAAGCTGGTTAT
AAAAAACCAGCGATTTCACAAGGAACGAGAGCAGCCACCCAGATTTGCACAACCTGGCTCCTTTGAGTATGAATATGCCA
TGCGCTGGAAGGCACTCACTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACCGCAACATCAAGGAGGCTCGTGAGAAG
CCGGAGATGGAGATGGAGGCTGCACGCCATAAGCACCAGGTCATGCTAATGAGACAGAATTTGACGAGGCGCCAAGAAGA
ACTTCGGAGGATGGAAGAGCTGCACAACCAAGAGGTGCAAAAACGAAAGCAACTGGAGCTCAGGCAGGAGGAAGGGCGCA
GGCGCCGTGAAGAAGAGATGCGGCGGCAGCAAGAAGAAACGATGCGGCGACAGCAGCAAGGATTCAAGCGAACCTTCCCT
GATGTGAGAGAGCAGGAGATTCGGATGGATCAGATGGCTATGGGAGGTGCTATGGGCATAAACAGCAGAGGTGCCTTGCC
CCCTGCTCCTGTGCCAGCTGGTACCCCGGCTCCTCCAGGACCTGCCACTATGATGCCGGATGGAACTTTGGGATTGACCC
CACAAACAACTGAACGCTTTGGTCAGGCTGCTACAATGGAAGGAATTGGGGCAATTTGTGGAACTCCGCCTGCATTCAAC
CATGCAGCTCCTGGAGCTGAATTTGCTCCAAACAAACGTCGCAGATAC

Alignment

ORF - retro_pabe_1398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQSNKTFNLEKQNHTPRKHHQHHHQQQHHQQQQQQPPPPPIPANGQQASSQNEGLTI-DLKNFRKPGEKT
          M.SNKTFNLEKQNHTPRK...........Q...QQPPPPPIPANGQQ.SSQNEGL.I.DLKNFRKPGEKT
Retrocopy MHSNKTFNLEKQNHTPRKXXXXXXXXHQQQ--HQQPPPPPIPANGQQVSSQNEGLAI>DLKNFRKPGEKT

Parental  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL
          FTQ.SRLFVGNLPPDITEEEMRKLF.KYGKAG.VFIHKD.GFGFIRLETRTLAEIAKVELDN.PL.GKQL
Retrocopy FTQ*SRLFVGNLPPDITEEEMRKLFKKYGKAGKVFIHKD*GFGFIRLETRTLAEIAKVELDNKPLCGKQL

Parental  RVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCS
          .V.F.CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIV.DRGRPSGKGIVEFSGKPAA.KALDRCS
Retrocopy CVHFSCHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVGDRGRPSGKGIVEFSGKPAAGKALDRCS

Parental  EGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEK
          EGSFLLTTF..PVT.EPMDQLDDEEGLPEKLVIKNQ.FHKEREQPPRFAQPGSFEYEYAMRWKAL.EMEK
Retrocopy EGSFLLTTFLCPVTMEPMDQLDDEEGLPEKLVIKNQRFHKEREQPPRFAQPGSFEYEYAMRWKALTEMEK

Parental  QQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERR
          QQQDQVDRNIKEAREK.EMEMEAARH.HQVMLMRQ.L.RRQEELRRMEELHNQEVQKRKQLELRQEE.RR
Retrocopy QQQDQVDRNIKEAREKPEMEMEAARHKHQVMLMRQNLTRRQEELRRMEELHNQEVQKRKQLELRQEEGRR

Parental  RREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPASQGPATM
          RR.................GFK.TFPD.REQEIRM.QMAMGGAMGIN.RGA.PPAPVPAGTPA..GPATM
Retrocopy RRXXXXXXXXXXXXXXXXQGFKRTFPDVREQEIRMDQMAMGGAMGINSRGALPPAPVPAGTPAPPGPATM

Parental  MPDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
          MPDGTLGLTP.TTERFGQAATMEGIGAI.GTPPAFN.AAPGAEFAPNKRRRY
Retrocopy MPDGTLGLTPQTTERFGQAATMEGIGAICGTPPAFNHAAPGAEFAPNKRRRY

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	12.83 RPM	65.91 RPM
SRP007412_cerebellum	14.59 RPM	64.57 RPM
SRP007412_heart	5.96 RPM	26.76 RPM
SRP007412_kidney	15.11 RPM	83.33 RPM
SRP007412_liver	12.55 RPM	54.47 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1398 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1398 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1398 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1699
Pan troglodytes	retro_ptro_1150
Gorilla gorilla	retro_ggor_1273

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016057	2 retrocopies	retro_amel_1438, retro_amel_795,
Bos taurus	ENSBTAG00000012152	2 retrocopies	retro_btau_1027, retro_btau_313,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Equus caballus	ENSECAG00000008502	2 retrocopies	retro_ecab_357, retro_ecab_427,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Homo sapiens	ENSG00000147140	1 retrocopy	retro_hsap_1699,
Gorilla gorilla	ENSGGOG00000006194	1 retrocopy	retro_ggor_1273,
Microcebus murinus	ENSMICG00000000232	1 retrocopy	retro_mmur_569,
Myotis lucifugus	ENSMLUG00000002489	1 retrocopy	retro_mluc_622,
Mustela putorius furo	ENSMPUG00000004937	1 retrocopy	retro_mputfur_937,
Mus musculus	ENSMUSG00000031311	2 retrocopies	retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys	ENSNLEG00000001278	1 retrocopy	retro_nleu_1344,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii	ENSOGAG00000004834	3 retrocopies	retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii	ENSPPYG00000020451	1 retrocopy	retro_pabe_1398 ,
Pan troglodytes	ENSPTRG00000022010	1 retrocopy	retro_ptro_1150,
Pteropus vampyrus	ENSPVAG00000016503	1 retrocopy	retro_pvam_444,
Rattus norvegicus	ENSRNOG00000003689	2 retrocopies	retro_rnor_1178, retro_rnor_1503,
Sorex araneus	ENSSARG00000007959	2 retrocopies	retro_sara_661, retro_sara_663,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,