RetrogeneDB ID: retro_nleu_2042

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397324.1:12936127..12936792(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC2
• Ensembl ID: ENSNLEG00000009274
• Aliases: None
• Description: None

Sequence

>retro_nleu_2042
ACTGACGTTGAGGCAGGGATGAAATTTGATGGGGAAAAATGTAAGTATTAAATTCAGATTCCCATGCTTTATAAGATTGA
CCCAACAATTACCACGATGCCGGTGGAGTAAAAACCTGATGTCATATACAGTGGTGTTGTTGGCTGTAGGGAACAGATTG
AGACATTGTAAGTAGTTGAAACCCCACTACTTCATCCAGAGAGATTTGTTAACCTTGGCATGGAGACTCCCAAGAGTGTG
CTCTTTGGTCCACTAGGTGCAGGCAAGACACTCTGTGCTTAGGTGGTTGCTAAATAGGACTGATGCTTGCTTCATCGAGT
TATTGGATATGAACGTTTACAGAAATATATCTGCAAAGGGGCTGGAATGGTTCATGAGCTCTTCCCAGTGGCCAGAACGA
GAAATGCCTGCCTTATCTTCTTTGATGAAACTGATGCTATTGGAAGAGCTCAGTTTGATGATGGTGCTGGAGGTGACAAT
GAAGTACAGAGAAAAATGTGGGAACTAATTCATCAGTTGGATGGCTTTGACCCTCAAGGCAATATTAAGTGCTGATGGCC
ACTAACAGACGTGATACTTTGGATTCAGCACTGATGAAGCCAGGGAAATTGGAAAGAAAGATTGAATTTAGTTTACCTGA
TCCAGAGGGTCAGACTCACATCTTT

Alignment

ORF - retro_nleu_2042 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.69 %
• Parental protein coverage: 51.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERF
          TD.E.GM.......KY.I.IP...KIDPT.T.M.VE.KPDV.YS.V.GC.EQIE.L..VVETPLLHPERF
Retrocopy TDVEAGMKFDGEKCKY*IQIPMLYKIDPTITTMPVE*KPDVIYSGVVGCREQIETL*-VVETPLLHPERF

Parental  VNLGIEPPKGVLLFGPPGTGKTLCARAVA-NRTDACFI-RVIGSELVQKYVGEGARMVRELFEMARTKKA
          VNLG.E.PK.VL.FGP.G.GKTLCA..VA.NRTDACFI.RVIG.E..QKY...GA.MV.ELF..ART..A
Retrocopy VNLGMETPKSVL-FGPLGAGKTLCA*VVA>NRTDACFI<RVIGYERLQKYICKGAGMVHELFPVARTRNA

Parental  CLIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIK-VLMATNRPDTLDPALMRPGRLD
          CLIFFDE.DAIG.A.FDDGAGGDNEVQR.M.ELI.QLDGFDP.GNIK.VLMATNR.DTLD.ALM.PG.L.
Retrocopy CLIFFDETDAIGRAQFDDGAGGDNEVQRKMWELIHQLDGFDPQGNIK<VLMATNRRDTLDSALMKPGKLE

Parental  RKIEFSLPDLEGRTHIF
          RKIEFSLPD.EG.THIF
Retrocopy RKIEFSLPDPEGQTHIF

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_2042 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005729	1 retrocopy	retro_etel_1316,
Homo sapiens	ENSG00000161057	2 retrocopies	retro_hsap_2705, retro_hsap_3980,
Gorilla gorilla	ENSGGOG00000009167	3 retrocopies	retro_ggor_1885, retro_ggor_2672, retro_ggor_2673,
Myotis lucifugus	ENSMLUG00000008853	1 retrocopy	retro_mluc_1642,
Macaca mulatta	ENSMMUG00000003432	2 retrocopies	retro_mmul_1538, retro_mmul_2299,
Monodelphis domestica	ENSMODG00000017238	1 retrocopy	retro_mdom_868,
Mustela putorius furo	ENSMPUG00000018268	3 retrocopies	retro_mputfur_1025, retro_mputfur_232, retro_mputfur_387,
Nomascus leucogenys	ENSNLEG00000009274	2 retrocopies	retro_nleu_1578, retro_nleu_2042 ,
Otolemur garnettii	ENSOGAG00000005164	2 retrocopies	retro_ogar_2198, retro_ogar_2309,
Pongo abelii	ENSPPYG00000017883	2 retrocopies	retro_pabe_2257, retro_pabe_2412,
Pan troglodytes	ENSPTRG00000019553	2 retrocopies	retro_ptro_1826, retro_ptro_2702,
Tarsius syrichta	ENSTSYG00000000666	4 retrocopies	retro_tsyr_1031, retro_tsyr_1272, retro_tsyr_1857, retro_tsyr_2178,
Vicugna pacos	ENSVPAG00000008921	1 retrocopy	retro_vpac_44,