RetrogeneDB ID: retro_nleu_889

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:24815819..24816569(-)
• Located in intron of: ENSNLEG00000015338

Retrocopy information

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

Parental gene information

• Parental gene symbol: FYTTD1
• Ensembl ID: ENSNLEG00000015547
• Aliases: None
• Description: None

Sequence

>retro_nleu_889
ATGAGAATACAATGGGTACTCCAACAGAATTCTGGTTTTGGTAAACCAGTCTAAGCTGCAGAGGAAGAGTAATGCCTGGA
AAGAGACATCCTCATGGATAATCATTGGCCTTGCAGTTAGAAAGTCATCTGGAATTGGAAAAGGAATTAGTCCTATGAAT
TGTCCACATCTAAGTGACAAGAATACAGAACACTATTTTCCAGTGTTAAAAAGAAAGGCAAGCCTTCTGAAACAAAATGA
AGTGCATAGAAAACCAGCTGCAGTTCTCAAGAGACCTAACCAGCTAAACAGAAAAAATAACATTATGTCCAATTTTACCA
AGAGAGGAAATAAATTAAGCCATCAGAAAGACACTTCACAGGTAACTTTTCTTTTCGGAAGAGGCCTGAAGAAGGTTCAG
GCCCAGTTGAACACGGAACAACTGCTAGATGATGTAGTAACAAAGAGAACTAGTCAGCACCAGACTTCTATCACAAACAC
AGGAATTTGACTGTATCTATTGATAACTCTGGAACAGTACCATGCCCAGCAACTGAGAAACCATGATTAATTCATATTGC
TATACCTTCATTCTTTAAAACACGGCAGCAAGAGAATGTAAAGAAAGTTCCAATGGGTGTTCCCCTACAATTTGACATAA
ATAGTATTAGAAAACAGATAGAGATGGCTTTGAATGAGCAGTTTGGGATCCTGAGAAAACAAAGAGCCACTCTCACATAT
AACAAAGGAGGAAGTCACTTTTTAACTGTG

Alignment

ORF - retro_nleu_889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 99.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRVRWGIQQNSGFGK-TSLNRRGRVMPGKRRPNG-VITGLAARKTTGIRKGISPMNRPPLSDKNIEQYFP
          MR..W..QQNSGFGK.TSL..RGRVMPGKR.P.G..I.GLA.RK..GI.KGISPMN.P.LSDKN.E.YFP
Retrocopy MRIQWVLQQNSGFGK<TSLSCRGRVMPGKRHPHG<IIIGLAVRKSSGIGKGISPMNCPHLSDKNTEHYFP

Parental  VLKRKANLLRQNEGQRKPVAVLKRPNQLSRKNNIPANFTRSGNKLNHQKDTRQATFLFRRGL-KVQAQLN
          VLKRKA.LL.QNE..RKP.AVLKRPNQL.RKNNI..NFT..GNKL.HQKDT.Q.TFLF.RGL.KVQAQLN
Retrocopy VLKRKASLLKQNEVHRKPAAVLKRPNQLNRKNNIMSNFTKRGNKLSHQKDTSQVTFLFGRGLKKVQAQLN

Parental  TEQLLDDVVAKRTRQWRTSTTNGGI-LTVSIDNPGAVQCPVTQKPRLTRTAVPSFLTKREQSDIKKVPKG
          TEQLLDDVV.KRT.Q..TS.TN.GI.LTVSIDN.G.V.CP.T.KP.L...A.PSF...R.Q...KKVP.G
Retrocopy TEQLLDDVVTKRTSQHQTSITNTGI<LTVSIDNSGTVPCPATEKP*LIHIAIPSFFKTRQQENVKKVPMG

Parental  VPLQFDINSVGKQTGMTLNERFGILKEQRATLTYNKGGSRFVTV
          VPLQFDINS..KQ..M.LNE.FGIL..QRATLTYNKGGS.F.TV
Retrocopy VPLQFDINSIRKQIEMALNEQFGILRKQRATLTYNKGGSHFLTV

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_889 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.

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889 ,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,