RetrogeneDB ID: retro_nleu_490

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397266.1:31149685..31151043(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC7
• Ensembl ID: ENSNLEG00000011230
• Aliases: None
• Description: None

Sequence

>retro_nleu_490
CAAGATTACAACAAAGCTTATAACTATTAGACAAAAGCCACAGATATGTGCCCTAGAAATGCTAGCTATCATAGTAATAG
AGCAGCTACATTGATGATGCCTGGAAGGTTCTGCGAAGCCCTTGGAGATACTTTCACAGTCAGTGAAATTGGATGATGGT
TTCTTCCGGGGACATCTACGAGAGGGCAAGTGCCACCTCTCTCCAGGGAATGCCATGGCAGCACATTGCAGTTTTCAGAG
AGCCCTAGAACTGGATCATAACAATGCTCACTCACAACAGGAGTTCACAAATGCTAATGCAGTCGAGGAATAGGAGAAAG
TCATAGAAACAGGTTTTGAGAAGTGGGCTTTTCAGAAGGTTGTTTTCTGCATGGACTATGCCCTAGAATTTGCCCCTGTC
TGCCATCACTTCAATATCCCTCAAAGCAGAATGTTTAGCAATGCTGTATCATTATCCAGAAGCACAGTCTGTGGCCAGTG
ACATTTTATGAATGGATTCCACCAATGTGGATGCTCTGTATGTACACAGACTTTGCCTTTATTATTAAGATTGTAGTCAG
TAGGCAGTTGTTCAGTTTTTTGTACAGGCTCTCAGAATGGCTCCTGACCATGAGAAGGCCTGCCTTGCGTGCAGAAATGC
CAGAACACTTAACGCAAAGAAACAAGACTGGAATAAAGCATTTAGGGAAGGAAATTACAAACTAGCTGATGAACTGTACA
CAGAAACCCCGGGATAGACCCCAACAACATAAAAGCAATTGCTAAACTCTACTGTAACCGGGATATGGTTAATTCCGAGC
TTGGGAAACTAGATGATGCAATAGACAGCTGCACAAATGCAGTGAAGCTCATGACACTTACATAAAAGCCTACTTGAGAA
GAGCTCAGAGTTTCATGGACACAGAACAGTATGAAGAAACAGTGAGAGGCTATGAAAAAAGTATATCAGATGGAGAAAAC
AAAAGAATACAAACAGCTCCTAAAAAATGCACAGCTGGAACTGAAGAAGAGTAAGAGGGATAATTACTACAAGGTTCTGG
AAGTAGACAAGAATGCCTCTGAGGACAAGATCAAGAAAGCTTATTGGAAACAGCCTTGATGTACCATCCACATCAGCTTG
ATGGAGCCAGTGCTGGGGTTCAAGAGGAGGAGGAGAAGATCAAGGAAGTGGCGAGGTCTTTACCATCCTCTTTGATTCCA
AGAAAATGGTTCATTATCACAGTGGACAGGACCTGGATAAGGAGGACATGAATTTGGGTGATTTTGATGCAAACAATATC
TTCAAGGTATTCTTCCGTGGTCCTACGGGCTTCAGCTGTGAAGCTTCTGGTCCAAGGAGTTTCTTTCTTCAATTGGGT

Alignment

ORF - retro_nleu_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.92 %
• Parental protein coverage: 96.59 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KDYNEAYNYYTKAIDMCPKNASYYGNRAATLMMLGRFREALGDA-QQSVRLDDSFVRGHLREGKCHLSLG
          .DYN.AYNY.TKA.DMCP.NASY..NRAATLMM.GRF.EALGD...QSV.LDD.F.RGHLREGKCHLS.G
Retrocopy QDYNKAYNY*TKATDMCPRNASYHSNRAATLMMPGRFCEALGDT>SQSVKLDDGFFRGHLREGKCHLSPG

Parental  NAMAACRSFQRALELDHKNAQAQQEFKNANAVMEYEKIAETDFEKRDFRKVVFCMDRALEFAPACHRFKI
          NAMAA..SFQRALELDH.NA..QQEF.NANAV.E.EK..ET.FEK..F.KVVFCMD.ALEFAP.CH.F.I
Retrocopy NAMAAHCSFQRALELDHNNAHSQQEFTNANAVEE*EKVIETGFEKWAFQKVVFCMDYALEFAPVCHHFNI

Parental  -LKAECLAMLGRYPEAQSVASDILRMDSTNADALYVRGLCLYYEDCIEKA-VQFFVQALRMAPDHEKACI
          .LKAECLAML..YPEAQSVASDIL.MDSTN.DALYV..LCLYY.DC...A.VQFFVQALRMAPDHEKAC.
Retrocopy >LKAECLAMLYHYPEAQSVASDIL*MDSTNVDALYVHRLCLYY*DCSQ*AVVQFFVQALRMAPDHEKACL

Parental  ACRNAKALKAKKEDGNKAFKEGNYKLAYELYTEA-LGIDPNNIKTNAKLYCNRGTVNSKLRKLDDAIEDC
          ACRNA..L.AKK.D.NKAF.EGNYKLA.ELYTE...GIDPNNIK..AKLYCNR..VNS.L.KLDDAI..C
Retrocopy ACRNARTLNAKKQDWNKAFREGNYKLADELYTET<PGIDPNNIKAIAKLYCNRDMVNSELGKLDDAIDSC

Parental  TNAVKL-DDTYIKAYLRRAQCYMDTEQYEEAVRDYE-KVYQTEKTKEHKQLLKNAQLELKKSKRKDYYKI
          TNAVKL..DTYIKAYLRRAQ..MDTEQYEE.VR.YE.KVYQ.EKTKE.KQLLKNAQLELKKSKR..YYK.
Retrocopy TNAVKL<HDTYIKAYLRRAQSFMDTEQYEETVRGYE>KVYQMEKTKEYKQLLKNAQLELKKSKRDNYYKV

Parental  LGVDKNASEDEIKKAYRKR-ALMHHPDRHSGASAEVQKEEEKKFKEV-GEAFTILSDPKKKTRYDSGQDL
          L.VDKNASED.IKKAY.K..ALM.HP....GASA.VQ.EEE.K.KEV.GE.FTIL.D.KK...Y.SGQDL
Retrocopy LEVDKNASEDKIKKAYWKQ<ALMYHPHQLDGASAGVQ-EEEEKIKEV<GEVFTILFDSKKMVHYHSGQDL

Parental  DEEGMNMGDFDPNNIFKAFFGGPGGFSFEASGPGNFFFQFG
          D.E.MN.GDFD.NNIFK.FF.GP.GFS.EASGP..FF.Q.G
Retrocopy DKEDMNLGDFDANNIFKVFFRGPTGFSCEASGPRSFFLQLG

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_490 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 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490 ,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,