RetrogeneDB ID: retro_nleu_1351

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397290.1:2463431..2464324(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBCH
• Ensembl ID: ENSNLEG00000006646
• Aliases: None
• Description: None

Sequence

>retro_nleu_1351
AAAAGGGGGAGTACAGGACTCATAACACTAAACAGACCAAAGTTCCTAAATGCACTGACTCTTCATATGATTTGGCAGAT
TTATCCATAGCTAGAGAAGTGGGAACAAGATCCTGAAACTCTCCTGATCATTATAAAAGGAGCCGGAGGAAAGGCTTTCT
GTGCTGGGAGTGATATAGAGTGATCTCGGAAGCTGAAAAGGCAAAACAGAAGATAGCACCAATTTTCTTCAGAGAAGAAT
ATATGCTGAACAATGCTTTTGGTTCTTGTCAGAAACGTTATGTTGCACTTATTCATGGAATTACAGTGTGTGGGGGAGTT
GGTCTGTCAGTCCATGGGCAGCTTCGAGTGGCTACAGAAAAGTATCTTTTTGCCATGCCAAAAACGGCACTAGGACTGTT
CCCTGATGTGGATGGAGGTTATTTCTTGCCACGAGTTCAAGGAAAACTCGGTTACTTCCTTGCATTAACAGGATTCAGAG
TAAAATGAAAGGATGTGTACAGAACAGGAATTGCTACACACTTCGTAGATTCTGAAAAGTTGGGCATGTTAGAGGAAGAT
TTGTTAGCCTTGAAATCACCTTCTAAAGAAAATATTGCAGCTGTCTTAGAAAATTACCATATGGAGTCTAAGATTGATGA
AGACAAGTCTTTTATACTTGAGGAACACATGGGCAAAATAAACAGTTGCTTTTCAGCCAATACTGTGGGACAAATTGTTG
AAAACTTACAGCAAGATGGTTCATCTTTTGCCCTAGAGCAATTGAAGGTAATTAATAACATGTCTCTGACATCTCTAAAG
ATCACACTAAGGTAACTCCTGGAGGGGTCTTGAAAGACCTTGGAAGAAGTACTAACTGTGGAGTATCAGCTAAGTCAAGC
TTGTATGGGGGGT

Alignment

ORF - retro_nleu_1351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 77.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKGCAGVITLNRPKFLNALTLNMIRQIYPQLKKWEQDPETFLIIIKGAGEKAFCAGGDI-RVISEAEKAK
          K.G..G.ITLNRPKFLNALTL.MI.QIYP.L.KWEQDPET.LIIIKGAG.KAFCAG.DI.RVISEAEKAK
Retrocopy KRGSTGLITLNRPKFLNALTLHMIWQIYP*LEKWEQDPETLLIIIKGAGGKAFCAGSDI<RVISEAEKAK

Parental  QKIAPVFFREEYMLNNAVGSCQKPYVALIHGITMGGGVGLSVHGQFRVATEKCLFAMPETAIGLFPDVGG
          QKIAP.FFREEYMLNNA.GSCQK.YVALIHGIT..GGVGLSVHGQ.RVATEK.LFAMP.TA.GLFPDV.G
Retrocopy QKIAPIFFREEYMLNNAFGSCQKRYVALIHGITVCGGVGLSVHGQLRVATEKYLFAMPKTALGLFPDVDG

Parental  GYFLPRLQGKLGYFLALTGFRLKGRDVYRAGIATHFVDSEKLAMLEEDLLALKCPSKENIASVLENYHTE
          GYFLPR.QGKLGYFLALTGFR.K..DVYR.GIATHFVDSEKL.MLEEDLLALK.PSKENIA.VLENYH.E
Retrocopy GYFLPRVQGKLGYFLALTGFRVK*KDVYRTGIATHFVDSEKLGMLEEDLLALKSPSKENIAAVLENYHME

Parental  SKIDRDKSFILEEHMDKINSCFSANTVEEIIENLQQDGSSFALEQLKVINKMSPTSLKITLKQLMEGSSK
          SKID.DKSFILEEHM.KINSCFSANTV..I.ENLQQDGSSFALEQLKVIN.MS.TSLKITL..L.EGS.K
Retrocopy SKIDEDKSFILEEHMGKINSCFSANTVGQIVENLQQDGSSFALEQLKVINNMSLTSLKITLR*LLEGS*K

Parental  TLQEVLTMEYRLSQACMRG
          TL.EVLT.EY.LSQACM.G
Retrocopy TLEEVLTVEYQLSQACMGG

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_1351 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000003341	1 retrocopy	retro_fcat_890,
Homo sapiens	ENSG00000198130	1 retrocopy	retro_hsap_3285,
Gorilla gorilla	ENSGGOG00000004988	1 retrocopy	retro_ggor_1317,
Macaca mulatta	ENSMMUG00000007283	1 retrocopy	retro_mmul_2062,
Mus musculus	ENSMUSG00000041426	1 retrocopy	retro_mmus_294,
Nomascus leucogenys	ENSNLEG00000006646	1 retrocopy	retro_nleu_1351 ,
Pongo abelii	ENSPPYG00000013021	2 retrocopies	retro_pabe_2714, retro_pabe_2827,
Pan troglodytes	ENSPTRG00000012741	1 retrocopy	retro_ptro_2222,
Tupaia belangeri	ENSTBEG00000004132	1 retrocopy	retro_tbel_3398,