RetrogeneDB ID: retro_nleu_1071

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397280.1:14894143..14894751(+)
• Located in intron of: ENSNLEG00000016766

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMYND19
• Ensembl ID: ENSNLEG00000009236
• Aliases: None
• Description: None

Sequence

>retro_nleu_1071
CACCAGTGGCTGTAGCTTCTGGTAGGAGAAGAGTAGTAGAGGCAGTATGCAGTCAGATAAAGACCAAATACACTGATAGA
TGAGCAAAGATATCCTGCTGGTGGAGAGATACCCCTCTGAGGTCCAAATGGAAGTAGATGCAGATGGAAATGGTACTAAG
ATATTCAGGTATGCTTTTGACAAGCACTGAGGAAGAGGATGGGGAAGACTCCTTCATGAGTTGCTGTGGGAGCACAGAAG
AGGCATGACCCCTGGGTTCCAGGTGGCACATCTCAATGCCCTGACTGAGGACAATTGCCTGGACAACCTGTAGCTGGTGC
TGTGGGGCTGGTGGCCCAAACCCAAAGAGACCTCCAGAAGAGGGAGCAAAGCTTGTACTGGCTTGCAATTCAGCAGCTTC
CCATGGACCCCAAAGAAGAGCAGTGACCTGTCCTAACTGTGACCTGGTACTATAACACCAATGGAGATGTGGTGGAAGAG
TTGAATTCTTACACCTACTATAGTAGCATTACCCTTCCTGCACAGTGATTGAGAAGTAGCTCCAGGAGTTCAACATCTGT
GGGTGCTGCCAGGTGGCCCGGTACTGAGGCTCTGAGTGCCAGCAGGAG

Alignment

ORF - retro_nleu_1071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.45 %
• Parental protein coverage: 71.53 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HQRLQFLVGER-SRGSVRRRQTKY-TLIDEQ-DIPLVESYSFEARMEVDADGNGAKIFAYAFDKNRGRGS
          HQ.L..LVGE..SRGS.........TLIDEQ.DI.LVE.Y..E..MEVDADGNG.KIF.YAFDK..GRG.
Retrocopy HQWL*LLVGEE>SRGSMQSDKDQI<TLIDEQ>DILLVERYPSEVQMEVDADGNGTKIFRYAFDKH*GRGW

Parental  GRLLHELLWERHRGGVAPGFQVVHLNAVTVDNRLDNLQLVPWGWRPKAEETSSKQREQSLYWLAIQQLPT
          GRLLHELLWE.HR.G..PGFQV.HLNA.T.DN.LDNL.LV.WGW.PK..ET.S.........L.....P.
Retrocopy GRLLHELLWE-HRRGMTPGFQVAHLNALTEDNCLDNL*LVLWGWWPKPKET-SRRGSKACTGLQFSSFPW

Parental  DP-IEEQFPVLNVTRYYNANGDVVEEEENSCTYYEC-HYPPCTVIEKQLREFNICGRCQVARYCGSQCQQ
          .P..EEQ.PVL.VT.YYN.NGDVV.EE.NS.TYY...HYP.CTVIEK.L.EFNICG.CQVARY.GS.CQQ
Retrocopy TP<KEEQ*PVLTVTWYYNTNGDVV-EELNSYTYYSS<HYPSCTVIEK*LQEFNICGCCQVARY*GSECQQ

Parental  K
          .
Retrocopy E

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_1071 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006644	2 retrocopies	retro_dnov_1389, retro_dnov_1468,
Dipodomys ordii	ENSDORG00000008360	1 retrocopy	retro_dord_390,
Equus caballus	ENSECAG00000012412	1 retrocopy	retro_ecab_903,
Echinops telfairi	ENSETEG00000005023	1 retrocopy	retro_etel_1068,
Homo sapiens	ENSG00000165724	1 retrocopy	retro_hsap_1367,
Gorilla gorilla	ENSGGOG00000006875	1 retrocopy	retro_ggor_1065,
Macropus eugenii	ENSMEUG00000011727	1 retrocopy	retro_meug_2010,
Macaca mulatta	ENSMMUG00000019610	1 retrocopy	retro_mmul_2195,
Monodelphis domestica	ENSMODG00000017172	1 retrocopy	retro_mdom_764,
Mus musculus	ENSMUSG00000026974	3 retrocopies	retro_mmus_1433, retro_mmus_2466, retro_mmus_942,
Nomascus leucogenys	ENSNLEG00000009236	1 retrocopy	retro_nleu_1071 ,
Tursiops truncatus	ENSTTRG00000010812	1 retrocopy	retro_ttru_900,