RetrogeneDB ID: retro_nleu_1520

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397297.1:15987506..15988635(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000139180
• Ensembl ID: ENSNLEG00000003252
• Aliases: None
• Description: None

Sequence

>retro_nleu_1520
ATGGCGGCTGCTGCACAATCCCGGGTTGTCTGGGCCCTGCCAATGTCACATTCTGCCATTACTGCAATAGCCACATCCGT
GTGTCACAGCCCACTCCATTGCCAGCTTCATCATGCCCTCATACCTCATGGGAAAGGTGGATGTTCCTCAAATCAGTGGG
ATTGTGGCCACTGGGTTTGGAGCAACAGGATTCCTGGGCCAATGTGTTGTCAACCACCTTGGATACGTGGGGTCACAGGT
GATCATACCCTATCGGTGTGATACATGTGACATCATGCACCTTTGTCCCATGGGAGACCTGGGCTAGCTTCTGTTTCTGG
AATGGGATGTGAGAGATAAAGATTCTATCCGACGAGTAGTGGAACACAGCAATGTGGTCATAAATCTTGTTGGATGAGAC
TGGGAAACCAAAAGCTTTGATTTTGAGGATGTTTTTGTGAAGATTCCCCAAGCAATTGCTCAGGTGTCCAAAGAAGCTGA
AGTTGGAAAATTCGTTCATGTTGCGCATCTGAATGTGAATATTAAAAGCTCTTCTAGATATTTGAGAAATAAGGCTGTTG
GAGAGAAAGCAGTGAGAGATGCATTTCCAGAAGCCATTATCGTAAAGCTGTTGGACATCTTTGGAAGAGAGGATAGATTC
CTTAATTATTTTGCAAATATGTGTTGGTTTGGTGCTATACCCCATGTTTCCTTGGGCTGGAAGGCAGTTAAACAACCAGT
ATATGTCGTAGATGTATCCAAAGGAATTGTTAATGCAGTTAAGGATCCTGATGCCAACGGGAAAACCTTTGCTTTTGTTG
GGCCAAATCGGTACCTCCTCTTTGACCTGGTGAAGTACATCTTTGCTGTGGCTCACAGACTCTTCCCCCCGTACCCCTTG
CCACCTTTTTCCTATCAGTGGGTAGCAAGAGACTTTGAAATAAGCCCATTTGAGTCCTGGACAACAAGGGATAAAGTGGA
GCATATTCACATCACAGGCATGACCTTGTCTCACCTGCCCAGCTTAGAAGACCTTGGTATTCAGGCAACACCACTGGAAC
TCAAGGCCATCGAGGTGCTGCAGCTTCATCACACTTATTGCTGGCTGTCTGCTGAAATTGAGGATGTGAAGCCGGCCAAG
ACCGTCAAC

Alignment

ORF - retro_nleu_1520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAAQSRVVRVLSMSRSAVTAIATSVCHGPPCRQLHHALIPHGKGGRSS-VSGIVTTVFGATGFLGRYV
          MAAAAQSRVV..L.MS.SA.TAIATSVCH.P...QLHHALIPHGKGG.SS..SGIV.T.FGATGFLG..V
Retrocopy MAAAAQSRVVWALPMSHSAITAIATSVCHSPLHCQLHHALIPHGKGGCSS>ISGIVATGFGATGFLGQCV

Parental  VNHLGRMGSQVIIPYRCDTYDIMHLRPMGDLGQLLFLEWDARDKDSIRRVVEHSNVVINLIGRDWETKNF
          VNHLG..GSQVIIPYRCDT.DIMHL.PMGDLG.LLFLEWD.RDKDSIRRVVEHSNVVINL.G.DWETK.F
Retrocopy VNHLGYVGSQVIIPYRCDTCDIMHLCPMGDLG*LLFLEWDVRDKDSIRRVVEHSNVVINLVG*DWETKSF

Parental  DFEDVFVKIPQAIAQLSKEAGVEKFIHVSHLNANIKSSSKYLRNKAVGEKVVRDAFPEAIIIKPSDIFGR
          DFEDVFVKIPQAIAQ.SKEA.V.KF.HV.HLN.NIKSSS.YLRNKAVGEK.VRDAFPEAII.K..DIFGR
Retrocopy DFEDVFVKIPQAIAQVSKEAEVGKFVHVAHLNVNIKSSSRYLRNKAVGEKAVRDAFPEAIIVKLLDIFGR

Parental  EDRFLNSFASMHRFGPTPLGSLGWKTVKQPVYVVDVSKGIVNAVKDPDANGKSFAFVGPNRYLLFHLVKY
          EDRFLN.FA.M..FG..P..SLGWK.VKQPVYVVDVSKGIVNAVKDPDANGK.FAFVGPNRYLLF.LVKY
Retrocopy EDRFLNYFANMCWFGAIPHVSLGWKAVKQPVYVVDVSKGIVNAVKDPDANGKTFAFVGPNRYLLFDLVKY

Parental  IFAVAHRLFLPFPLPLFAYRWVARVFEISPFEPWITRDKVERVSICVXXXXXXXXXXDLGIQATPLELKA
          IFAVAHRLF.P.PLP.F.Y.WVAR.FEISPFE.W.TRDKVE...I............DLGIQATPLELKA
Retrocopy IFAVAHRLFPPYPLPPFSYQWVARDFEISPFESWTTRDKVEHIHITGMTLSHLPSLEDLGIQATPLELKA

Parental  IEVLRRHRTYRWLSAEIEDVKPAKTVD
          IEVL..H.TY.WLSAEIEDVKPAKTV.
Retrocopy IEVLQLHHTYCWLSAEIEDVKPAKTVN

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_1520 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000009588	1 retrocopy	retro_acar_16,
Danio rerio	ENSDARG00000070723	1 retrocopy	retro_drer_1,
Homo sapiens	ENSG00000139180	1 retrocopy	retro_hsap_2585,
Gorilla gorilla	ENSGGOG00000006076	1 retrocopy	retro_ggor_1618,
Macaca mulatta	ENSMMUG00000020813	1 retrocopy	retro_mmul_648,
Monodelphis domestica	ENSMODG00000018283	1 retrocopy	retro_mdom_209,
Nomascus leucogenys	ENSNLEG00000003252	1 retrocopy	retro_nleu_1520 ,
Otolemur garnettii	ENSOGAG00000005225	1 retrocopy	retro_ogar_2244,
Pongo abelii	ENSPPYG00000004171	1 retrocopy	retro_pabe_1905,
Pan troglodytes	ENSPTRG00000004557	1 retrocopy	retro_ptro_1511,
Ictidomys tridecemlineatus	ENSSTOG00000006504	1 retrocopy	retro_itri_543,