RetrogeneDB ID: retro_nleu_1350

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397290.1:323258..323729(-)
• Located in intron of: ENSNLEG00000010815

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTIF3
• Ensembl ID: ENSNLEG00000000343
• Aliases: None
• Description: mitochondrial translational initiation factor 3 [Source:HGNC Symbol;Acc:29788]

Sequence

>retro_nleu_1350
TCAAAGGAGCCTGCAGAAGACCAGCTCATGACAGGAAGGCAGACCCGCCAGGAACGGCTGAGGCTGAGAGAGATGGAGAA
GGGTAACCCCAAAACTGGACCAACCCTGACAAAGGAACTGACTTTTTCTTCAAACGTTGGACAACAGGATTTGAAGGCAA
AGACTAAACAGATTCAGCCGTGGATTAAGAAAAAACACCAAGTTCGAATTACTATAAAGAAAGGAGAAAATGTAGACGAG
TCGGAAAATAAAGTGGAGGAGATATTCCATCAAATACTCCAGACTGTGCCTGGAATAGCTACATTCTCATCCAGGCCACA
AGCTGTTCAAGGAGGAAAAGCTTTAATGTGGGTTCTTTGTCCTTTGAGCAAAAAGGAAGAGAAGGCATATCGAGAAACTC
AAGAGACCCAGGAAAGAGACACTTTGAACGAAGACCATGGAAATGATAATGAATCAAATGTTCCGCATCAG

Alignment

ORF - retro_nleu_1350 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.17 %
• Parental protein coverage: 61.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SIEPAEYQLMTGLQILQERQRLREMEKASPKTGPTLRKELTLSSNIGQHDLDTKTKQIQQWIKKKHLVRI
          S.EPAE.QLMTG.Q..QER.RLREMEK..PKTGPTL.KELT.SSN.GQ.DL..KTKQIQ.WIKKKH.VRI
Retrocopy SKEPAEDQLMTGRQTRQERLRLREMEKGNPKTGPTLTKELTFSSNVGQQDLKAKTKQIQPWIKKKHQVRI

Parental  TIKKGKNVDMSENEMEEIFHQILQTMPGIATFSSRPQAVQGGKALMCVLRALSKNEEKAYRETQETQERD
          TIKKG.NVD.SEN..EEIFHQILQT.PGIATFSSRPQAVQGGKALM.VL..LSK.EEKAYRETQETQERD
Retrocopy TIKKGENVDESENKVEEIFHQILQTVPGIATFSSRPQAVQGGKALMWVLCPLSKKEEKAYRETQETQERD

Parental  TLNKDHGNDKESNVLHQ
          TLN.DHGND.ESNV.HQ
Retrocopy TLNEDHGNDNESNVPHQ

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_1350 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004404	1 retrocopy	retro_chof_466,
Homo sapiens	ENSG00000122033	1 retrocopy	retro_hsap_3284,
Gorilla gorilla	ENSGGOG00000008409	1 retrocopy	retro_ggor_1318,
Nomascus leucogenys	ENSNLEG00000000343	1 retrocopy	retro_nleu_1350 ,
Oryctolagus cuniculus	ENSOCUG00000011721	1 retrocopy	retro_ocun_533,
Pongo abelii	ENSPPYG00000005236	1 retrocopy	retro_pabe_2713,
Pan troglodytes	ENSPTRG00000005732	1 retrocopy	retro_ptro_2221,
Tupaia belangeri	ENSTBEG00000012276	3 retrocopies	retro_tbel_4048, retro_tbel_4602, retro_tbel_760,