RetrogeneDB ID: retro_nleu_2818

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397439.1:609868..611306(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000008474
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDC73
• Ensembl ID: ENSNLEG00000018050
• Aliases: None
• Description: None

Sequence

>retro_nleu_2818
AGGCCAACCTACACATTGGATTCCATTTTATTTCTGCTTAATAATGTGCACCTTTCTCATCCTGTTTATGTCCGACGTGC
AGCTACTGAAAATATTCCTGTGGTTAGAAGACCTGATCGAAAAGATCTACTTGGATATCTCAATGGTGAAGCGTCAACAT
CGGCAAGTATAGACAGAAGTGCTCCCTTAGAAATAGGTCTTCAGCGATCTACTCAAGTCAAACGAGCTGCAGATGAAGTT
TTAGAAGAAGCAAAGAAACCACGAATTGAGGATGAAGAGTGTGTGCGCCTTGATAAAGAAAGATTGGCTGCCCGTTTGGA
GGGTCACAAAGAAGGGATTGTACAGACTGAACAGATTAGGTCTTTGTCTGAAGCTATGTCAGTGGAAAAAATTGCTGCAA
TCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGACATAACTGCCCTTAAACAGAGG
AGTTTTGTGGATGCTGAGGTAGATGTGACCCGAGATATTGTCAGCAGAGAGAGTATGGAGGACACGAACAACTATCTTAC
AAAGCACAGGAAAGAATTTTTCCAAGAACATTTTTGCAATTCTTCAATCTGTAAAAGCCAGAGAAGAAGGGCGTGCACCT
GAACAGCGACCTGCCCCAAATGCAGCACCTGTGGATCCCACTTTGCGCACCAAACAGCCTATGCCAGCTGCCTATAACAG
ATACGATCAGGAAAGATTCAAAGGAAAAGAAGAAACGGAAGGCTTCAAAATTGACACTATGGGAACCTACCATGGTATGA
CACTGAAATCTGTAACGGAGGGTGCATCTGCCCGGAAGACTCAGACTCCTGCAGCCCAGCCAGTACCAAGACCAGTTTCT
CAAGCAAGACCTCCCCCAAATCAGAAGAAAGGATCTTGAACACCCATTATCATAATTCCTGCAGCTACCACCTCTTTAAT
AACCATGCTTAATACAAAAGACCTTCTGCAGGACCTGAAATTTGTCCCATCAGATGAAAAGAAGAAACAAGGTTGTCAAC
GAGAAAATGAAACTCTAATACAAAGAAGAAAAGACCAGATGCAACCAGGGGGCACTGCAATTAGTGTTACAGTACCTTAT
AGAGTAGTAGACCAGCCCCTTAAACTTATGCCTCAAGACTGGGACCGCGTTGTAGCTATTTTTGTGCAGGGTCCTGCATG
GCAGTTCAAAGGTTGGCCGTGGCTTTTGCCTGATGGATCACCAGTTGATCTATTTGCTAAAATTAAAGCCTTCCATCTGA
AGTATGATGAAGTTCGTCTGGATCCAAATGTTCAGAAATGGGATGTAACAGTATTAGAACTCAGCTACCACAAACGTCAT
TTGGATAGACCAGTGTTCTTACGGTTTTGGGAAACATTGGACAGGTACATGGTAAAGCATACATCCCACTTGAGATTC

Alignment

ORF - retro_nleu_2818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.22 %
• Parental protein coverage: 90.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  REYYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRSAPLEIGLQRS
          R..YTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRSAPLEIGLQRS
Retrocopy RPTYTLDSILFLLNNVHLSHPVYVRRAATENIPVVRRPDRKDLLGYLNGEASTSASIDRSAPLEIGLQRS

Parental  TQVKRAADEVLAEAKKPRIEDEECVRLDKERLAARLEGHKEGIVQTEQIRSLSEAMSVEKIAAIKAKIMA
          TQVKRAADEVL.EAKKPRIEDEECVRLDKERLAARLEGHKEGIVQTEQIRSLSEAMSVEKIAAIKAKIMA
Retrocopy TQVKRAADEVLEEAKKPRIEDEECVRLDKERLAARLEGHKEGIVQTEQIRSLSEAMSVEKIAAIKAKIMA

Parental  KKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNF-SKNIFAILQSVKARE
          KKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRE....T....L....K.F.SKNIFAILQSVKARE
Retrocopy KKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRESMEDT-NNYLTKHRKEF>SKNIFAILQSVKARE

Parental  EGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASAR
          EGRAPEQRPAPNAAPVDPTLRTKQP.PAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASAR
Retrocopy EGRAPEQRPAPNAAPVDPTLRTKQPMPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASAR

Parental  KTQTPAAQPVPRPVSQARPPPNQKKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKKQGCQRE
          KTQTPAAQPVPRPVSQARPPPNQKKGS.TPIIIIPAATTSLITMLN.KDLLQDLKFVPSDEKKKQGCQRE
Retrocopy KTQTPAAQPVPRPVSQARPPPNQKKGS*TPIIIIPAATTSLITMLNTKDLLQDLKFVPSDEKKKQGCQRE

Parental  NETLIQRRKDQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQGPAWQFKGWPWLLPDGSPVDIF
          NETLIQRRKDQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVA.FVQGPAWQFKGWPWLLPDGSPVD.F
Retrocopy NETLIQRRKDQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAIFVQGPAWQFKGWPWLLPDGSPVDLF

Parental  AKIKAFHLKYDEVRLDPNVQKWDVTVLELSYHKRHLDRPVFLRFWETLDRYMVKHKSHLRF
          AKIKAFHLKYDEVRLDPNVQKWDVTVLELSYHKRHLDRPVFLRFWETLDRYMVKH.SHLRF
Retrocopy AKIKAFHLKYDEVRLDPNVQKWDVTVLELSYHKRHLDRPVFLRFWETLDRYMVKHTSHLRF

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_2818 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008675	2 retrocopies	retro_chof_2535, retro_chof_747,
Myotis lucifugus	ENSMLUG00000012093	2 retrocopies	retro_mluc_1439, retro_mluc_2152,
Monodelphis domestica	ENSMODG00000012222	1 retrocopy	retro_mdom_263,
Nomascus leucogenys	ENSNLEG00000018050	1 retrocopy	retro_nleu_2818 ,
Oryctolagus cuniculus	ENSOCUG00000016332	1 retrocopy	retro_ocun_302,
Otolemur garnettii	ENSOGAG00000000351	1 retrocopy	retro_ogar_767,