RetrogeneDB ID: retro_nleu_2009

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397322.1:14420501..14420798(+)
• Located in intron of: ENSNLEG00000010241

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP1C
• Ensembl ID: ENSNLEG00000009356
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:G1RDV4]

Sequence

>retro_nleu_2009
ATGGGAGTGCAGGTGGAAACCATCTCCCCAGGAGATGGGCGCACATTCCCGAAGCACGGCCAGACCTGCGTGGTGCACTA
TACCGGGATGCTTGAAGATGGAAAGAAATTTGATTCCTCCCGGGACAGAAAAAAGCCCTTTAAGTTTATGCTAGGCAAGC
AGGAGGTGATCCGAGGCTGGGAAGAAGGGGTTGCCCAGATGAGTGTGGGTCAGAGAGCCAAACTGACTATATCTCCAGAT
GATGCCTATAGTGCCACTGGGCACCCAGGCATCATCCCACCACATGCCACTCTTCTT

Alignment

ORF - retro_nleu_2009 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.95 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVG
          MGVQVETISPGDGRTFPK.GQTCVVHYTGMLEDGKKFDSSRDR.KPFKFMLGKQEVIRGWEEGVAQMSVG
Retrocopy MGVQVETISPGDGRTFPKHGQTCVVHYTGMLEDGKKFDSSRDRKKPFKFMLGKQEVIRGWEEGVAQMSVG

Parental  QRAKLTISPDYAYGATGHPGIIPPHATLV
          QRAKLTISPD.AY.ATGHPGIIPPHATL.
Retrocopy QRAKLTISPDDAYSATGHPGIIPPHATLL

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_2009 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Callithrix jacchus	ENSCJAG00000020908	4 retrocopies	retro_cjac_1544, retro_cjac_3889, retro_cjac_4157, retro_cjac_537,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Homo sapiens	ENSG00000088832	1 retrocopy	retro_hsap_1198,
Gorilla gorilla	ENSGGOG00000001729	3 retrocopies	retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733,
Nomascus leucogenys	ENSNLEG00000000800	1 retrocopy	retro_nleu_1406,
Nomascus leucogenys	ENSNLEG00000002835	1 retrocopy	retro_nleu_2291,
Nomascus leucogenys	ENSNLEG00000009356	5 retrocopies	retro_nleu_2009 , retro_nleu_2628, retro_nleu_2728, retro_nleu_2730, retro_nleu_604,
Otolemur garnettii	ENSOGAG00000002629	1 retrocopy	retro_ogar_673,
Pan troglodytes	ENSPTRG00000013163	2 retrocopies	retro_ptro_2983, retro_ptro_818,
Sus scrofa	ENSSSCG00000007188	1 retrocopy	retro_sscr_98,
Tursiops truncatus	ENSTTRG00000003547	3 retrocopies	retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos	ENSVPAG00000011511	1 retrocopy	retro_vpac_171,