RetrogeneDB ID: retro_nleu_1175

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397283.1:25385574..25386518(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT7
• Ensembl ID: ENSNLEG00000010414
• Aliases: None
• Description: None

Sequence

>retro_nleu_1175
TTGAAGCTTCTTGAAGTTGTCCATCCTGCAGCAAAGACTTCAATGAACATTGCCAAATATCAAGATGCTGAGGTGGGTGA
TGGCACCACCTCAGTGACTTTGCTGGCTGCAGAGTTTCTGAAGCAGGTGAAACCTTATGTGGAGGAAGCTTTGCACCCAA
AGATCATCATTCAAGCTTTACACACAGCCATCCAATTGGCAGTTAATGATAACAAAGAGATCACTGTGACCATGAAGAAG
ACAGAAATAGTGGAGCAGAAGAAGCTGCTTGGAGAAGTGTGCCATCCTGCTCTGAGCTCCAAGCTCATCTCCCAGCAGAA
AGCCTTCTTTTCAAAGATGGTGGTTGATGCAGTGATGATGCTTGATGGTTTGCTGCAGCTTAAAGTGATTGGAATCAAGA
AGATACAGGGTGGAGCCGTAGAGGATTCCCATCTGTTAGCTGGTGCCGCATTCAAGAATTTCTTTTATGCTGGGTTGGAA
ATGCAACCCCAAAAGTGCCATAATCCCAAGATTGCACTTTTAAATTTTGAGCTTGAGTTGAAAGTTAGGAGAGATAATGC
TGAGATCAGAGTCCTCACAATGGGGAATTACCAGGCAATTGTTGATGCTGAGTGGAACATTCTCTACGACAAGTAAGCAA
GGATCCATCATTCTGGAGCCAAAGTTGTCTTGTCCAAACTCTCCAGTGGGGATGTGGTCACTCAGTACTTTGCTGACAGG
GGCAAGTTCTGTGCTGGCCGAGTACCTGAGAAGGATCTGAATAGGACAATGATGGCCTACAGAGGGTCAATCCAGACCAT
TGTGAATGCTCTGTCAGCAGACATGCTGGGCAGATGCCAGGTGTTTGAGGAGACCCTGACTGGAAGTGAGAGGCACAATT
TCTTTACTGGCCTCCCAAGGCCAAGACATGCACCTTTATCCTCCACAGTGATGCCACAACTTAT

Alignment

ORF - retro_nleu_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.66 %
• Parental protein coverage: 59.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKLLDVVHPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNK
          LKLL.VVHPAAKT...IAK.QDAEVGDGTTSVTLLAAEFLKQVKPYVEE.LHP.III.A..TA.QLAVN.
Retrocopy LKLLEVVHPAAKTSMNIAKYQDAEVGDGTTSVTLLAAEFLKQVKPYVEEALHPKIIIQALHTAIQLAVND

Parental  IKEIAVTVKKADKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVEAVMMLDDLLQLKMIGIKKVQGGAL
          .KEI.VT.KK...VEQ.KLL......ALSSKLISQQKAFF.KMVV.AVMMLD.LLQLK.IGIKK.QGGA.
Retrocopy NKEITVTMKKTEIVEQKKLLGEVCHPALSSKLISQQKAFFSKMVVDAVMMLDGLLQLKVIGIKKIQGGAV

Parental  EDSQLVAGVAFKKTFSYAGFEMQPKKYHNPKIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILY
          EDS.L.AG.AFK..F.YAG.EMQP.K.HNPKIALLN.ELELK...DNAEIRV.T...YQAIVDAEWNILY
Retrocopy EDSHLLAGAAFKNFF-YAGLEMQPQKCHNPKIALLNFELELKVRRDNAEIRVLTMGNYQAIVDAEWNILY

Parental  DKLEKIHHSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADVLGRC
          DK...IHHSGAKVVLSKL..GDV.TQYFADR..FCAGRVPE.DL.RTMMA..GSIQT.VNALSAD.LGRC
Retrocopy DK*ARIHHSGAKVVLSKLSSGDVVTQYFADRGKFCAGRVPEKDLNRTMMAYRGSIQTIVNALSADMLGRC

Parental  QVFEETQIGGERYNFFTGC-PKAKTCTFILRGGAEQF
          QVFEET..G.ER.NFFTG..PKAKTCTFIL...A...
Retrocopy QVFEETLTGSERHNFFTGL<PKAKTCTFILHSDATTY

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_1175 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
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151,
Cavia porcellus	ENSCPOG00000019869	1 retrocopy	retro_cpor_1458,
Homo sapiens	ENSG00000135624	1 retrocopy	retro_hsap_3354,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093,
Nomascus leucogenys	ENSNLEG00000010414	1 retrocopy	retro_nleu_1175 ,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Pongo abelii	ENSPPYG00000012297	1 retrocopy	retro_pabe_2760,
Pan troglodytes	ENSPTRG00000012060	1 retrocopy	retro_ptro_2133,
Rattus norvegicus	ENSRNOG00000015630	2 retrocopies	retro_rnor_2179, retro_rnor_535,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708, retro_tbel_3751,