RetrogeneDB ID: retro_ggor_1273

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 16:59958014..59959281(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NONO
• Ensembl ID: ENSGGOG00000006194
• Aliases: None
• Description: None

Sequence

>retro_ggor_1273
ATGCAGAGTAATAAAACTTTTAACTTGGAGAAGCAAAACCATACTCCAAGAAAGCATCATCAACATCACCACCAGCAGCA
ACAGCTGCAGCCGCCACCACCGCCAATACCTGCGAATGGGCAACAGGCCAGCAGCCAAAATGAAGGCTTGACTATTTGAC
CTGAAGAATTTTAGAAAACCAGGAGAGAAGACCTTCACCCAACGAAGCCGTCTTCTTGTGGGAAATCTTCCTCCCGACAT
CACTGAGGAAGAAATGAGGAAACTATTTGAGAAATATGGAAAGGCAGGCAAAGTCTTCATTCATAAGGATTAAGGATTTG
GCTTTATCCGCTTGGAAACACGAACCCTAGCGGAGATTGCGAAAGTGGAGCTGGACAATATGCCACTCTGTGGAAAGCAG
CTGCGTGTGCGCTTTTCCTGCCATGGTGCATCCCTTACAGTTCGAAACCTTCCTCAGTATGTGTCCAACGAAGTGCTGGA
AGAAGCCTTTTCTGTGTTTGGCCAGGTAGAGAGGGCTGTAGTCATTGTGGATGATCGAGGAAGGCCCTCAGGAAAAGGCA
TTGTTGAGTTCTCAGGGAAGCCAGCTGCTGGGAAAGCTCTGGACAGACGCAGTGAAGGCTCCTTCCTGCTAACCACATTT
CCTCGTCCTGTGACTATGGAGCCCATGGACCAGTTAGATGATGAAGGGGGACTTCCAGAGAAGCTGGTTATAAAAAACCA
GCAATTTCACAAGGAACGAGAGCAACCACGCAGATTTGCACAGCCTGGCTCCTTTGAGTATGAATATGCCATGCGCTGGA
AGGCACTCATTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACCGCAACATCAAGGAGGCTCGTGAGAAGCCAGAGATG
GAGATGGAGGCTGCACGCCATAAGCACCAGGTCATGCTAACGAGACAGAATTTGATGAGGCGCCAAGAAGAACTTCGGAG
GATGGAAGAGCTGCACAACCAAGAGGTGCAAAAACGAAAGCAACTGTAGCTCAGGCAGGAGGAAGAGCGCAGGCGCCGTG
AAGAAGAGACACGGAGGCAGCAAGAAGAAATGATGCAGCCACAGCAGGAAGGATTCAAGGGAACCTTCCCTGATGTGAGA
GAGCAGGAGATTTGGATGGGTCAGATGGCTATGGGAGGTGCTATGGGCATAAACAGCAGAGGTGCCTTGCCCCCTGCTCC
TGTGCCAGCTGGTACCCCAGCTCCTCCAGGACCTGCCACTATGATGCCAGATGGAACTTTGGGATTG

Alignment

ORF - retro_ggor_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQSNKTFNLEKQNHTPRK----HHQHH---PPPPPIPANGQQASSQNEGLTI-DLKNFRKPGEKTFTQRS
          MQSNKTFNLEKQNHTPRK....HHQ.....PPPPPIPANGQQASSQNEGLTI.DLKNFRKPGEKTFTQRS
Retrocopy MQSNKTFNLEKQNHTPRKHHQHHHQQQQLQPPPPPIPANGQQASSQNEGLTI>DLKNFRKPGEKTFTQRS

Parental  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA
          RL.VGNLPPDITEEEMRKLFEKYGKAG.VFIHKD.GFGFIRLETRTLAEIAKVELDNMPL.GKQLRVRF.
Retrocopy RLLVGNLPPDITEEEMRKLFEKYGKAGKVFIHKD*GFGFIRLETRTLAEIAKVELDNMPLCGKQLRVRFS

Parental  CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSFL
          CH.ASLTVRNLPQYVSNE.LEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAA.KALDR.SEGSFL
Retrocopy CHGASLTVRNLPQYVSNEVLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAAGKALDRRSEGSFL

Parental  LTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQ
          LTTFPRPVT.EPMDQLDDE.GLPEKLVIKNQQFHKEREQP.RFAQPGSFEYEYAMRWKALIEMEKQQQDQ
Retrocopy LTTFPRPVTMEPMDQLDDEGGLPEKLVIKNQQFHKEREQPRRFAQPGSFEYEYAMRWKALIEMEKQQQDQ

Parental  VDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRREEE
          VDRNIKEAREK.EMEMEAARH.HQVML.RQ.LMRRQEELRRMEELHNQEVQKRKQL.LRQEEERRRREEE
Retrocopy VDRNIKEAREKPEMEMEAARHKHQVMLTRQNLMRRQEELRRMEELHNQEVQKRKQL*LRQEEERRRREEE

Parental  MRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPGPATMMPDGT
          .RRQQEEMM..QQEGFKGTFPD.REQEI.MGQMAMGGAMGIN.RGA.PPAPVPAGTPAPPGPATMMPDGT
Retrocopy TRRQQEEMMQPQQEGFKGTFPDVREQEIWMGQMAMGGAMGINSRGALPPAPVPAGTPAPPGPATMMPDGT

Parental  LGL
          LGL
Retrocopy LGL

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	6.19 RPM	70.92 RPM
SRP007412_cerebellum	8.16 RPM	82.74 RPM
SRP007412_heart	1.75 RPM	19.79 RPM
SRP007412_kidney	7.28 RPM	79.24 RPM
SRP007412_liver	5.99 RPM	51.49 RPM
SRP007412_testis	4.04 RPM	71.90 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1273 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1699
Pan troglodytes	retro_ptro_1150
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,