RetrogeneDB ID: retro_nleu_1933

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397317.1:7281103..7281800(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6ORF106
• Ensembl ID: ENSNLEG00000008387
• Aliases: None
• Description: None

Sequence

>retro_nleu_1933
AACCTACGAGCAGCAATTGGTGCCTATTGTGACTTTGATAGCCCAAACATCAGTGTGCCCTCTATGTCCTTTGTTGAAGA
TGTCACCAAAGGAGAAGCAGAGTCAATACCTCCTGATACTTAGTTTGTAAAATCACGGTAGATGCAGAATTCTGGCACAA
AGGCCTGGCTTCCAGGGGTTTGTCTTAAGTATGTTGGGGGAGACCAATTTGGACATGTGAACGTGGTGATAGTGAGAGCG
CTAGAAGCCCCTCAAAATTGCAGATGTCAGCGTCCAGACGTGCAGCTCCAGCAGAGCAGGAATGTATCAGGGACAGTGGT
GAATGTGCATTGCTACAGGACTCTGCTATGAAGCTGTTACCAGGAAGATTCTCAATGTAAAGGTGGGTGGACTTTTAGGA
GTAATGCAGCTGCCGTCATCTTTTGAAACGCAGCTCAATGCACCGCTGCATCCCAAGGTAGAAGGAAACTTCAATCAGTT
TGCCTCTTCCCAAAAGAACGAAGAATCACATGAAAACAACTTAAAAGACCCTGGGGGTTCCGGGTTCCACCCAATCAGTG
AAAACACACAAGCTCCTGCTCCTGACCAAACAGAACAAGATCAGAATAGACTCACAGAACTCTGTAAATCTGCCCCCAGT
GGTCACGCAAACAGCTTATCAGTAGTAAGGCTCCACGGGCCTTAGTCCTTCAGGCAG

Alignment

ORF - retro_nleu_1933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.01 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLQAAIGAYYDFESPNISVPSMSFVEDVTIGEGESIPPDTQFVKTWRIQNSGAEAWPPGVCLKYVGGDQF
          NL.AAIGAY.DF.SPNISVPSMSFVEDVT.GE.ESIPPDT.FVK....QNSG..AW.PGVCLKYVGGDQF
Retrocopy NLRAAIGAYCDFDSPNISVPSMSFVEDVTKGEAESIPPDT*FVKSR*MQNSGTKAWLPGVCLKYVGGDQF

Parental  GHVNMVMVRSLE-PQEIADVSVQMCSPSRAGMYQGQWRMCTATGLYYGDVIWVILSVEVGGLLGVTQQLS
          GHVN.V.VR.LE.P..IADVSVQ.CS.SRAGMYQGQW.MC.ATGL.Y..V...IL.V.VGGLLGV.Q..S
Retrocopy GHVNVVIVRALE>PLKIADVSVQTCSSSRAGMYQGQW*MCIATGLCYEAVTRKILNVKVGGLLGVMQLPS

Parental  SFETEFNTQPHRKVEGNFNPFASPQKNRQSDENNLKDPGGSEFDSISKNTWASAPDQTEQDQNRLSQNSV
          SFET..N...H.KVEGNFN.FAS.QKN..S.ENNLKDPGGS.F..IS.NT.A.APDQTEQDQNRL.....
Retrocopy SFETQLNAPLHPKVEGNFNQFASSQKNEESHENNLKDPGGSGFHPISENTQAPAPDQTEQDQNRLTE-LC

Parental  NLSPSSHANNLSVVTYSKGLHGPYPFGQ
          ...PS.HAN.LSVV.....LHGP..F.Q
Retrocopy KSAPSGHANSLSVVR----LHGP*SFRQ

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_1933 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034493	1 retrocopy	retro_btau_1343,
Callithrix jacchus	ENSCJAG00000015304	1 retrocopy	retro_cjac_2788,
Homo sapiens	ENSG00000196821	1 retrocopy	retro_hsap_2137,
Gorilla gorilla	ENSGGOG00000000388	1 retrocopy	retro_ggor_1653,
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Macaca mulatta	ENSMMUG00000022824	1 retrocopy	retro_mmul_2155,
Nomascus leucogenys	ENSNLEG00000008387	2 retrocopies	retro_nleu_1933 , retro_nleu_2739,
Otolemur garnettii	ENSOGAG00000011264	1 retrocopy	retro_ogar_3245,
Ochotona princeps	ENSOPRG00000009350	1 retrocopy	retro_opri_559,
Pongo abelii	ENSPPYG00000016519	2 retrocopies	retro_pabe_1265, retro_pabe_1928,
Pan troglodytes	ENSPTRG00000018068	1 retrocopy	retro_ptro_1564,