RetrogeneDB ID: retro_nleu_1489

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397296.1:14456397..14457774(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1A2
• Ensembl ID: ENSNLEG00000010060
• Aliases: None
• Description: Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:G1RGC3]

Sequence

>retro_nleu_1489
GTGGGAAAGGAAAAGACTCATATCAACATTGTCATCATCGGACACGTAGATTTGGGCAAGTTTACCACTACTGGCCATCT
GATCTACAAATGCGGTGACATCGACAAAAAAAATCATGGAGAAATTTGAGAAGGAGCCTGCTGAGATGGGAAAGGGCTCC
TTCAAGTATGCCTGGGTCTTGGATAAACTGAAAGCTGAGCGTGAACGTGGTATCACCATTGATATCTCCTTGTGGAAATT
TGAGACCAGTAAGTAGTACGTGACTATCATTAATGCCCCAGGACACAGAGACTTCATCAAAACCATGATTACAGGGACAT
CTCAGGCTGACTCTGCTGTCCTGATTGTTGCTGCTGGTGTTGGCGAATTTGAAGGTGGCATCTCCAGGAATGGGCAGACC
CAAGAGCATGCCCTTCTGGCTTACACACTGGGGGTGAAACAACTAATTGTTGGTGTTAACAAAATTGATTCCACTGAGCC
ACCCTACAGCTAGAAGAGATATGAGGCAATCAATTCCGCACCTTCATTAAGAAAATTGGCTACAACCCCGACACAATAGT
ATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGTTGGAGCCAACTGCTAACATACCTTGGTTCAAGGGATGGAAAG
TCACCCGTAAGGATGGCCATGTCAGTGGAACCATGCTGCTTGAGGCTCTGGACTACATCCTACCACCAAGTCGTCCAACT
GACAAGCCCTTGTGCCTGCCTCCCCAGGATGTCTACAAAATTGGTGGTATTGGTACTGTTCCTGTTGGCCAAGTGGAGAC
TGGTGTTCTCAAACCTGCTATGGTGGTCACCTTTGCTCCAGTCAACATTACAACCGAAGTAAAATCTGTCAAAATGCACC
ACGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAGCGTGGGCTTCAATGTCAACAATGTGTCTGTCAAGGATGTTTGTTGT
GGCAATGCTGTTGGTGACAGCAAAAATGACCCACCAGTGGAAGCAGCTGGCTTCACTGCTTAGGTGATTATCCTGAACCA
TCCAGGCCAAATCATCGTTGGCTGTGCCCGTGCACTGTATAGCCACATGGTTCACATTGCGTGCAAGTTTGCTGAGCTGA
AGGAAAAGATTGATCGCCGTGCTGGTACAAAGCTGGAAGATGGCCCTAAATTCTCGAAGTCTGGTGATGCTGCCAGCATT
GATACGGTTCCTGGCAAGCACATTTGTGTTGAAGGATTCTCAGACTATCCACCGCTGGGTGGCTTTGCTGTTCATGATAT
GAGACAGACAATTGCTGTGGGTGTCATCAAAGGAGTGGACAAGAAGGCTGCTGGAGATGGCAAAGTCACTTAGTCTGCCC
AGAAGGCTCAGAAAGCT

Alignment

ORF - retro_nleu_1489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.32 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRT-IEKFEKEAAEMGKGSFKYAWVLDKLKAERER
          .GKEKTHINIV.IGHVD.GK.TTTGHLIYKCG.ID.....EKFEKE.AEMGKGSFKYAWVLDKLKAERER
Retrocopy VGKEKTHINIVIIGHVDLGKFTTTGHLIYKCGDIDXXX>MEKFEKEPAEMGKGSFKYAWVLDKLKAERER

Parental  GITIDISLWKFETTKYYITIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALL
          GITIDISLWKFET.K.Y.TII.APGHRDFIK.MITGTSQAD.AVLIVAAGVGEFE.GIS.NGQT.EHALL
Retrocopy GITIDISLWKFETSK*YVTIINAPGHRDFIKTMITGTSQADSAVLIVAAGVGEFEGGISRNGQTQEHALL

Parental  AYTLGVKQLIVGVNKMDSTEPAYSEKRYDEIVKEVSAYIKKIGYNPA-TVPFVPISGWHGDNMLEPSPNM
          AYTLGVKQLIVGVNK.DSTEP.YS.KRY..I....S....K....P..T..FVPISGW.GDNMLEP..N.
Retrocopy AYTLGVKQLIVGVNKIDSTEPPYS*KRYEAINSAPS--LRKLATTPT<TIVFVPISGWNGDNMLEPTANI

Parental  PWFKGWKVERKEGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGILRPGMVV
          PWFKGWKV.RK.G..SG..LLEALD.ILPP.RPTDKPL.LP.QDVYKIGGIGTVPVG.VETG.L.P.MVV
Retrocopy PWFKGWKVTRKDGHVSGTMLLEALDYILPPSRPTDKPLCLPPQDVYKIGGIGTVPVGQVETGVLKPAMVV

Parental  TFAPVNITTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDIRRGNVCGDSKSDPPQEAAQFTSQVIILN
          TFAPVNITTEVKSV.MHHEALSEALPGD.VGFNV.NVSVKD...GN..GDSK.DPP.EAA.FT..VIILN
Retrocopy TFAPVNITTEVKSVKMHHEALSEALPGDSVGFNVNNVSVKDVCCGNAVGDSKNDPPVEAAGFTA*VIILN

Parental  HPGQISAGYSPVIDCHTAHIACKFAELKEKIDRRSGKKLEDNPKSLKSGDAAIVEMVPGKPMCVESFSQY
          HPGQI..G.......H..HIACKFAELKEKIDRR.G.KLED.PK..KSGDAA....VPGK..CVE.FS.Y
Retrocopy HPGQIIVGCARALYSHMVHIACKFAELKEKIDRRAGTKLEDGPKFSKSGDAASIDTVPGKHICVEGFSDY

Parental  PPLGRFAVRDMRQTVAVGVIKNVEKKSGGAGKVTKSAQKAQKA
          PPLG.FAV.DMRQT.AVGVIK.V.KK..G.GKVT.SAQKAQKA
Retrocopy PPLGGFAVHDMRQTIAVGVIKGVDKKAAGDGKVT*SAQKAQKA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1489 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Latimeria chalumnae	ENSLACG00000002952	1 retrocopy	retro_lcha_39,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Macropus eugenii	ENSMEUG00000005018	23 retrocopies	retro_meug_1067, retro_meug_110, retro_meug_1160, retro_meug_1240, retro_meug_1334, retro_meug_135, retro_meug_1421, retro_meug_1451, retro_meug_1465, retro_meug_1501, retro_meug_1662, retro_meug_1690, retro_meug_1710, retro_meug_1829, retro_meug_2023, retro_meug_2044, retro_meug_2050, retro_meug_316, retro_meug_601, retro_meug_755, retro_meug_792, retro_meug_850, retro_meug_920,
Myotis lucifugus	ENSMLUG00000016760	1 retrocopy	retro_mluc_1250,
Mustela putorius furo	ENSMPUG00000008289	3 retrocopies	retro_mputfur_1030, retro_mputfur_609, retro_mputfur_761,
Nomascus leucogenys	ENSNLEG00000001476	6 retrocopies	retro_nleu_1492, retro_nleu_1584, retro_nleu_1754, retro_nleu_1901, retro_nleu_235, retro_nleu_829,
Nomascus leucogenys	ENSNLEG00000010060	2 retrocopies	retro_nleu_11, retro_nleu_1489 ,
Ornithorhynchus anatinus	ENSOANG00000004908	1 retrocopy	retro_oana_73,
Otolemur garnettii	ENSOGAG00000004630	8 retrocopies	retro_ogar_1067, retro_ogar_2034, retro_ogar_2329, retro_ogar_2497, retro_ogar_2583, retro_ogar_3191, retro_ogar_3270, retro_ogar_643,
Ictidomys tridecemlineatus	ENSSTOG00000028862	1 retrocopy	retro_itri_1028,
Tursiops truncatus	ENSTTRG00000001835	1 retrocopy	retro_ttru_993,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,