RetrogeneDB ID: retro_nleu_1458

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397294.1:7676451..7677391(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSNLEG00000000295
• Aliases: None
• Description: None

Sequence

>retro_nleu_1458
GGCGGGTGGCCGGCATGGCTGGGGGCGGCCGGGCTGCTGGGCCCCGGACCTTGGCCTGCACCCTGTGCAGCCGCTCACTC
TCCTTCCTGCTGCAGGTGTACGCGCTGCTGCCCGGCCACACCGACACACTTCAACCCCGGAATCTTCCTCTTCTGCTGCT
GTGAGCCGCCATGCTGTGCTGGCCTGTGAGTTTTTACCAATCAGCTACCCAGGAAAAATGATTTTTACTCATATGGGCCC
ACCTTCTGAGAATCCTCCCCCAGAAACAGGACAATCAGTGTGTCTCTAACTTAAGTCTGGTGCTCACCTCTGCAGGGTTT
GTGGCTGTTTAGGCCCCAAAACGTGCTCCAGATGCCACAAAGCGTATTACTGCAGCAGGGAGCATCAGACCCTAGACCGG
AGATTGGCACATAAGCAGGCTTGTACACAACCAGATGCTTTGGATCATATAATTCCAGACCACGACTTCCTTTTTCCAGA
ATTTGCAATTGTAGTAGAAACAGAAGATGAAGATTACACCTGAGGTTGTGGAAAAGGAAGATTACTCAGAGATTATAGGG
AGCATGGGTGACACACTTGAAGAAGAACTGGATTGCATGGCAAAACATGAATCCAGGAAAGATAAAATTTTTCAGAAGTT
CAAAACTCAGATAGCCCTTGAACCAGAACAGATTCTCAGATATGGCAGAGGTATTGCCCCCATCTGGATTTCTGGTGAAA
ATATTCCTCAAGAAAAGGATATTCCAGAGAATATCCTTTGTGATGCCAAGAGAATGTTTGAATTCCAGGTATGCCTCAGC
TCCTAAACTACCTGAAGGCTGACAGACTGGGCAAGAGCATTGACTGGGGCATCCTGGCTGTCTTCACCTGGGCTGAGAGC
TGCAGCTTGGGTACTGGCTATACAGAATAATTTGTGTGGAAGCAGGATGTAACAGATACA

Alignment

ORF - retro_nleu_1458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.28 %
• Parental protein coverage: 90.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GGRPTWLSAAGL-PGPRALACELCGRPLSFLLQVYAPLPGRADA-FHRCIFLFCCREQPCCAGLRVFRNQ
          GG.P.WL.AAGL..GPR.LAC.LC.R.LSFLLQVYA.LPG..D..F...IFLFCC.E.PCCAGL.VF.NQ
Retrocopy GGWPAWLGAAGL<AGPRTLACTLCSRSLSFLLQVYALLPGHTDT>FNPGIFLFCCCEPPCCAGL*VFTNQ

Parental  LPRKNDFYSYEP-PSENPPPETGESVCLQLKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQTLDWRLGH
          LPRKNDFYSY.P.PSENPPPETG.SVCL.LKSGAHLCRVCGCLGPKTCSRCHKAYYCS.EHQTLD.RL.H
Retrocopy LPRKNDFYSYGP>PSENPPPETGQSVCL*LKSGAHLCRVCGCLGPKTCSRCHKAYYCSREHQTLDRRLAH

Parental  KQACAQPDHLDHIIPDHNFLFPEFEIVIETEDE-IMPEVVEKEDYSEIIGSMGEAPEEELDSMAKHESRE
          KQAC.QPD.LDHIIPDH.FLFPEF.IV.ETEDE.I.PEVVEKEDYSEIIGSMG...EEELD.MAKHESR.
Retrocopy KQACTQPDALDHIIPDHDFLFPEFAIVVETEDE>ITPEVVEKEDYSEIIGSMGDTLEEELDCMAKHESRK

Parental  DKIFQKFKTQIALEPEQILRYGRGIAPIWISGENIPQEKDIPD-CPCGAKRILEFQV-MPQLLNYLKADR
          DKIFQKFKTQIALEPEQILRYGRGIAPIWISGENIPQEKDIP....C.AKR..EFQV.MPQLLNYLKADR
Retrocopy DKIFQKFKTQIALEPEQILRYGRGIAPIWISGENIPQEKDIPENILCDAKRMFEFQV<MPQLLNYLKADR

Parental  LGKSIDWGILAVFTCAESCSLGTGYTEEFVWKQDVTDT
          LGKSIDWGILAVFT.AESCSLGTGYTE.FVWKQDVTDT
Retrocopy LGKSIDWGILAVFTWAESCSLGTGYTE*FVWKQDVTDT

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_1458 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017075	2 retrocopies	retro_amel_1329, retro_amel_1404,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458 , retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,