RetrogeneDB ID: retro_ptro_1150

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:69098156..69099555(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NONO
• Ensembl ID: ENSPTRG00000022010
• Aliases: None
• Description: non-POU domain containing, octamer-binding [Source:HGNC Symbol;Acc:7871]

Sequence

>retro_ptro_1150
ATGCAGAGTAATAAAACTTTTAACTTGGAGAAGCAAAACCATACTCCAAGAAAGCATCATCAACATCATCACCAGCAGCA
ACAGCTGCAGCCGCCACCACCGCCAATACCTGCAAATGGGCAACAGGCCAGCAGCCAAAATGAAGGCTTGACTATTTGAC
CTGAAGAATTTTAGAAAACCAGGAGAGAAGACCTTGACCCAACGAAGCCGTCTTTTTGTGGGAAATCTTCCTCCCGACAT
CACTGAGGAAGAAATGAGGAAACTATTTGAGAAATATGGAAAGGCAGGCGAAGTCTTCATTCATAAGGATTAAGGATTTG
GCTTTATCCGCTTGGAAACACGAACCCTAGCGGAGATTGCGAAAGTGGAGCTGGACGGTATGCCACTCTGTGGAAAGCAG
CTGCGTGTGCGCTTTTCCTGCCATAGTGCATCCCTTACAGTTCGAAACCTTCCTCAGTATGTGTCCAACGAAGTGCTGGA
AGAAGCCTTTTCTGTGTTTGGCCAGGTAGAGAGGGCTGTAGTCATTGTGGATGATCGAGGAAGGCCCTCAGGAAAAGGCA
TTGTTGAGTTCTCAGGGAAGCCAGCTGCTGGGAAAGCTCTGGACAGACGCAGTGAAGGCTCCTTCCTGCTAACCACATTT
CCTCGTCCTGTGACTATGGAGCCCATGGACCAGTTAGATGATGAAGGGGGACTTCCAGAGAAGCTGGTTATAAAAAACCA
GCAATTTCACAAGGAACGAGAGCAACCACCCAGATTTGCACAGCCTGGCTCCTTTGAGTGTGAATATGCCATGCGCTGGA
AGGCACTCATTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACCGCAACATCAAGGAGGCTCGTGAGAAGCCAGAGATG
GAGATGGAGGCTGCACGCCATAAGCACCAGGTCATGGTAATGAGACAGAATTTGATGAGGCGCCAAGAAGAACTTCGGAG
GATGGAAGAGCTGCACAACCAAGAGGTGCAAAAACGAAAGCAACTGGAGCTCAGGCAGGAGGAAGAGCGCAGGCGCCGTG
AAGAAGAGATGCGGCGGCAGCAAGAAGAAATGATGCAGCCACAGCAGGAAGGATTCAAGGGAACCTTCCCTGATGTGAGA
GAGCAGGAGATTTGGATGGGTCAGATGGCTATGGGAGGTGCTATGGGCATAAACAGCAGAGGTGCTTTGACCCCTGCTCC
TGTGCCAGCTGGTACCCCAGCTCCTCCAGGACCTGCCACTATGATGCCGGATGGAACTTTGGGATTGACCCCACCAACAA
CTGAACGCTTTGGTCAGGCTGCTACAATGGAAGGAATTGGGGCAATTGGTGAAACTCCTCCTGCATTCAACCATGCAGCT
CCTGGAGCTGAATTTGCTCCAAACAAACGTCGCCGATAC

Alignment

ORF - retro_ptro_1150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQSNKTFNLEKQNHTPRKHHQHHHQQQHHQQQQQQPPPPPIPANGQQASSQNEGLTI-DLKNFRKPGEKT
          MQSNKTFNLEKQNHTPRKHHQHHHQQQ....Q.Q.P.PPPIPANGQQASSQNEGLTI.DLKNFRKPGEKT
Retrocopy MQSNKTFNLEKQNHTPRKHHQHHHQQQ----QLQPP-PPPIPANGQQASSQNEGLTI>DLKNFRKPGEKT

Parental  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL
          .TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD.GFGFIRLETRTLAEIAKVELD.MPL.GKQL
Retrocopy LTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD*GFGFIRLETRTLAEIAKVELDGMPLCGKQL

Parental  RVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCS
          RVRF.CHSASLTVRNLPQYVSNE.LEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAA.KALDR.S
Retrocopy RVRFSCHSASLTVRNLPQYVSNEVLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAAGKALDRRS

Parental  EGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEK
          EGSFLLTTFPRPVT.EPMDQLDDE.GLPEKLVIKNQQFHKEREQPPRFAQPGSFE.EYAMRWKALIEMEK
Retrocopy EGSFLLTTFPRPVTMEPMDQLDDEGGLPEKLVIKNQQFHKEREQPPRFAQPGSFECEYAMRWKALIEMEK

Parental  QQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERR
          QQQDQVDRNIKEAREK.EMEMEAARH.HQVM.MRQ.LMRRQEELRRMEELHNQEVQKRKQLELRQEEERR
Retrocopy QQQDQVDRNIKEAREKPEMEMEAARHKHQVMVMRQNLMRRQEELRRMEELHNQEVQKRKQLELRQEEERR

Parental  RREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPGPATM
          RR..................FKGTFPD.REQEI.MGQMAMGGAMGIN.RGA..PAPVPAGTPAPPGPATM
Retrocopy RRXXXXXXXXXXXXXXXXXXFKGTFPDVREQEIWMGQMAMGGAMGINSRGALTPAPVPAGTPAPPGPATM

Parental  MPDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
          MPDGTLGLTPPTTERFGQAATMEGIGAIG.TPPAFN.AAPGAEFAPNKRRRY
Retrocopy MPDGTLGLTPPTTERFGQAATMEGIGAIGETPPAFNHAAPGAEFAPNKRRRY

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	0.18 RPM	66.28 RPM
SRP007412_cerebellum	0.22 RPM	178.45 RPM
SRP007412_heart	0.06 RPM	57.74 RPM
SRP007412_kidney	0.18 RPM	133.11 RPM
SRP007412_liver	0.20 RPM	114.96 RPM
SRP007412_testis	0.21 RPM	44.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1150 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1150 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1699
Gorilla gorilla	retro_ggor_1273
Pongo abelii	retro_pabe_1398

---

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,