RetrogeneDB ID: retro_nleu_2021

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397323.1:11876418..11876878(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPRKB
• Ensembl ID: ENSNLEG00000000300
• Aliases: None
• Description: None

Sequence

>retro_nleu_2021
TTAATATTATTTAAAGATGTAAAAAATGCAGGGAACTTGAGAAACAAAGCCATGGAAGGTATCATTGATGGCTCACTGAT
ACATCCTGCAGTGATTGTCAATTCATTTGAGATATTTGCAGCCACAAAGAAAGCAGTTTGCCTCTACAAACTGGGAGAAA
TGAATACAAGAGCTCTATCTACTGAAATTATTTTCAACCTTTCCCCAAATAACAATATTTCAGAGGCATTGAAAAAATGT
GGTATCTCAGCAAATGACACTTAAATTCCAATTGTTTATAGTAATGAGGGAGAAAAACAAATAAATCAAGGATATCTAAT
GTCTCAAATAGAAGGTCAGCAGGTTTCTCTGAAAAATCTTCCTGAAATAATAAATATTACAAAAGTCAAAAAGAAATATA
CACTCCCTCCACAAAAAGAAAGTATTGGGAACATTATTGGATGGTATTTGTAGAATGTCA

Alignment

ORF - retro_nleu_2021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 77.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLLFKDVKNAGDLRRKAMEGTIDGSLINPTVIVDPFQILVAANKAVHLYKLGKMKTRTLSTEIIFNLSPN
          L.LFKDVKNAG.LR.KAMEG.IDGSLI.P.VIV..F.I..A..KAV.LYKLG.M.TR.LSTEIIFNLSPN
Retrocopy LILFKDVKNAGNLRNKAMEGIIDGSLIHPAVIVNSFEIFAATKKAVCLYKLGEMNTRALSTEIIFNLSPN

Parental  NNISEALKKFGISANDTSILIVYIEEGEKQINQEYLISQVEGHQVSLKNLPEITNITEVKKIYKLSSQEE
          NNISEALKK.GISANDT.I.IVY..EGEKQINQ.YL.SQ.EG.QVSLKNLPEI.NIT.VKK.Y.L..Q.E
Retrocopy NNISEALKKCGISANDT*IPIVYSNEGEKQINQGYLMSQIEGQQVSLKNLPEIINITKVKKKYTLPPQKE

Parental  SI-GTLLDGIICRMS
          SI.GTLLDG.ICRMS
Retrocopy SI>GTLLDG-ICRMS

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_2021 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 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012021	1 retrocopy	retro_chof_35,
Callithrix jacchus	ENSCJAG00000004162	3 retrocopies	retro_cjac_1999, retro_cjac_2867, retro_cjac_3065,
Homo sapiens	ENSG00000144034	1 retrocopy	retro_hsap_552,
Gorilla gorilla	ENSGGOG00000009062	1 retrocopy	retro_ggor_501,
Macaca mulatta	ENSMMUG00000030805	1 retrocopy	retro_mmul_1571,
Monodelphis domestica	ENSMODG00000016950	2 retrocopies	retro_mdom_1264, retro_mdom_465,
Nomascus leucogenys	ENSNLEG00000000300	2 retrocopies	retro_nleu_2021 , retro_nleu_957,
Oryctolagus cuniculus	ENSOCUG00000016251	2 retrocopies	retro_ocun_519, retro_ocun_769,
Otolemur garnettii	ENSOGAG00000032893	2 retrocopies	retro_ogar_523, retro_ogar_849,
Pongo abelii	ENSPPYG00000012292	1 retrocopy	retro_pabe_509,
Pteropus vampyrus	ENSPVAG00000012419	1 retrocopy	retro_pvam_75,
Ictidomys tridecemlineatus	ENSSTOG00000016406	4 retrocopies	retro_itri_1613, retro_itri_453, retro_itri_918, retro_itri_919,
Tupaia belangeri	ENSTBEG00000014584	2 retrocopies	retro_tbel_33, retro_tbel_3630,
Vicugna pacos	ENSVPAG00000007934	2 retrocopies	retro_vpac_149, retro_vpac_192,