RetrogeneDB ID: retro_nleu_1718

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:12020801..12022019(+)
• Located in intron of: ENSNLEG00000006329

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSNLEG00000003791
• Aliases: None
• Description: None

Sequence

>retro_nleu_1718
AGAATATATGTAAGAGCTTTAAATGCTACCAAAATGGAATGAGTATTTGCAAAACCATTCCTTGCTTTGCTGGATGGTCA
CCAAGATGGAGTAAGTTGCTTGGCAAAGCATCCAAAGAACCTGGCTGCTGTCCTTTCTCGGGCATGTGATGGAGAAGTTA
GAATTTGGAACCTGACTCAACAGAAATGTATCCCTACAATACAAGCACATGAAGGCTTTGTGTAAGGAATATGTACTCAC
TTTTGTGGGACTTCTTTTTTCACTGTTGGTGGTGACAAAACTGTGAAACAATGGAAAATGGATGGGCCAGGCTATGGAGA
TGAGGAAGAGCCATTACATACAGCATTAGGAAAGACAGTGTATACTGGGGTTGATCATCACTGGAAAGAAGCTGTTTTTG
CCACATGTGGACAGCAAGTAGACATTTGGGATGAACAAAGAATTAATCCTATATGTTCAATGACCTGGGGATTTGACAGT
GTAAGTAGTGTTAAATTTAACTCAATTGAGACATTTCTCTTGGGAAGTTTTGCGTCTGATAGGAGTATAGTACTGTATGA
CATGAGGCAAGCTACTCCTTTGAAAAAGGTTATCTTAGATATGAGAACAAATACAATCTGTTGGAACCCTATGAAAGCTT
TCATTTTTACGTCAGCAAATGAAGATTATAACTTACATACTTTTGATATGTGTGCACTGGACACTCCTGTAATGTTCCAT
GTGGATCATGTATCTGCAGTGCCTGACGTGGATTACCCTCCCACTGGGGAAGAGTTTCTGTCTGCTAGTTTCGATAAAGC
TGTTTGAATCTTTCCTATAGACAAAAATCGAAGCAGGGAGGTATATCACACAAAGTGAATGCAACATGTTATCTGTGTAA
AATGGACTTCTGACAACAAGTATATTATGTGTGGATCTGATGAAATGAACGTTTGCCTATGGAAAGCTAATGCTTCTGAA
AAGTTTGGTGTGCTTACATCACGAGAAAAAGCCGAGGATTATAACTAGAAATTGAAGGAGAAATTTCAGCATCATCCTCA
TATAAAATGTATAGCTTGTCATGGACATCTACCAAAATCTATCTACAGCCAGATTCAGGAACAGCGCATCATGAAAGAAG
CTTGTCGAAGACAGGAAGTGAATCGTATTAAACACAGCAAGCCTGGATCTGTGCCAATTGTGTCAGAGAAGAAGAAACAC
ATAGGGGCAGTTGTAAAA

Alignment

ORF - retro_nleu_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.98 %
• Parental protein coverage: 68.17 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REYVRALNATKLERVFAKPFLASLDGHRDGVNCLAKHPKNLATVLSGACDGEVRIWNLTQRNCIRTIQAH
          R.YVRALNATK.E.VFAKPFLA.LDGH.DGV.CLAKHPKNLA.VLS.ACDGEVRIWNLTQ..CI.TIQAH
Retrocopy RIYVRALNATKME*VFAKPFLALLDGHQDGVSCLAKHPKNLAAVLSRACDGEVRIWNLTQQKCIPTIQAH

Parental  EGFVRGICTRFCGTSFFTVGDDKTVKQWKMDGPGYGDEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQV
          EGFV.GICT.FCGTSFFTVG.DKTVKQWKMDGPGYGDEEEPLHT.LGKTVYTG.DHHWKEAVFATCGQQV
Retrocopy EGFV*GICTHFCGTSFFTVGGDKTVKQWKMDGPGYGDEEEPLHTALGKTVYTGVDHHWKEAVFATCGQQV

Parental  DIWDEQRTNPICSMTWGFDSISSVKFNPIETFLLGSCASDRNIVLYDMRQATPLKKVILDMRTNTICWNP
          DIWDEQR.NPICSMTWGFDS.SSVKFN.IETFLLGS.ASDR.IVLYDMRQATPLKKVILDMRTNTICWNP
Retrocopy DIWDEQRINPICSMTWGFDSVSSVKFNSIETFLLGSFASDRSIVLYDMRQATPLKKVILDMRTNTICWNP

Parental  MEAFIFTAANEDYNLYTFDMRALDTPVMVHMDHVSAVLDVDYSPTGKEFVSASFDKSIRIFPVDKSRSRE
          M.AFIFT.ANEDYNL.TFDM.ALDTPVM.H.DHVSAV.DVDY.PTG.EF.SASFDK...IFP.DK.RSRE
Retrocopy MKAFIFTSANEDYNLHTFDMCALDTPVMFHVDHVSAVPDVDYPPTGEEFLSASFDKAV*IFPIDKNRSRE

Parental  VYHTKRMQHVICVKWTSDSRYIMCGSDEMNIRLWKANASEKLGVLTSREKAAKDYNQKLKEKFQHYPHIK
          VYHTK.MQHVICVKWTSD..YIMCGSDEMN..LWKANASEK.GVLTSREK.A.DYN.KLKEKFQH.PHIK
Retrocopy VYHTK*MQHVICVKWTSDNKYIMCGSDEMNVCLWKANASEKFGVLTSREK-AEDYN*KLKEKFQHHPHIK

Parental  RIARHRHLPKSIYSQIQEQRIMKEARRRKEVNRIKHSKPGSVPIVSEKKKHVVAVVK
          .IA.H.HLPKSIYSQIQEQRIMKEA.RR.EVNRIKHSKPGSVPIVSEKKKH..AVVK
Retrocopy CIACHGHLPKSIYSQIQEQRIMKEACRRQEVNRIKHSKPGSVPIVSEKKKHIGAVVK

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_1718 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001595	3 retrocopies	retro_amel_1453, retro_amel_1723, retro_amel_399,
Canis familiaris	ENSCAFG00000000663	3 retrocopies	retro_cfam_1309, retro_cfam_1533, retro_cfam_305,
Callithrix jacchus	ENSCJAG00000016181	2 retrocopies	retro_cjac_3083, retro_cjac_612,
Felis catus	ENSFCAG00000027256	1 retrocopy	retro_fcat_1840,
Homo sapiens	ENSG00000164934	1 retrocopy	retro_hsap_1498,
Gorilla gorilla	ENSGGOG00000015124	1 retrocopy	retro_ggor_1150,
Myotis lucifugus	ENSMLUG00000007375	1 retrocopy	retro_mluc_2048,
Nomascus leucogenys	ENSNLEG00000003791	1 retrocopy	retro_nleu_1718 ,
Otolemur garnettii	ENSOGAG00000002277	1 retrocopy	retro_ogar_305,
Pongo abelii	ENSPPYG00000018809	2 retrocopies	retro_pabe_1249, retro_pabe_3211,
Pan troglodytes	ENSPTRG00000020493	1 retrocopy	retro_ptro_1017,
Sarcophilus harrisii	ENSSHAG00000006588	1 retrocopy	retro_shar_507,