RetrogeneDB ID: retro_nleu_1765

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397308.1:5138496..5139241(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC39A14
• Ensembl ID: ENSNLEG00000015557
• Aliases: None
• Description: solute carrier family 39 (zinc transporter), member 14 [Source:HGNC Symbol;Acc:20858]

Sequence

>retro_nleu_1765
GAGATCTTGAAGATGTTTCTCAAAGAGGAAAATGAACATCACATAGACATAGTAGCCATTATGCCTCTGAGAGGCTTCCT
TCCAAGAAGCACCAGGAGGAGGGGGGTGATGGAGAAGCTGCATAATGGGGACCTGGACCACATGACCCCTCAGCACTGCA
ACAGTGAACTGGATGGCAAGCGGTCCATGATAGACGGGAAGGTCGTGGTGGGCTCACTCTCTGTGCTGGTCCTGCAGGCT
CCCCAGAGTGCCTGCTGGAGCTGAAAGGTGTCCACTACTTTATCAGCACTCTGGCCTGGGTGATCGCCCTGAGCAGCAGC
CTCCACAATGTCCTCAGCAGCCTGGCCATTGGCGCCTCCTTCACCATGTGTGTGGTCCAAGGCCTCGGCACCTGGTGGCC
ATCTTCCATGAGGAGTTCCCACATGACTTTGTCATCCTGCTTAGCGCTGGGAGGACCATTCAGCACTGTCTTCTTCAAAC
CCCTTCCACCTGCTGCTATGTGGGTCTGGCCTTTGGCATCCTGGCCAGCAGCCACTTCTCTGCCAGCTGGATTTTTGTGC
TGGTTGGAGGAATGTTCTTGAATACTGCTGTGGCTGATATGTTCCCTGAGACGAATGAGGTCTGCCAAGACGATGGAGGG
AAGGGCAGCAACTCCATCCCCTTTGTCATTCAGAACCTGGGCCTGTTGGCCAGATTCACCGTCATGCTGGTCCTCATGGT
GTGTTCAGGACAGATCCAGATTGGG

Alignment

ORF - retro_nleu_1765 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.95 %
• Parental protein coverage: 51.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KILKILLKQKNEHH-HGHS-HYASETLPSKKDQEEG-VMEKLQNGDLDHMIPQHCNSELDGKAPMVDEKV
          .ILK..LK..NEHH.H.HS.HYASE.LPSKK.QEEG.VMEKL.NGDLDHM.PQHCNSELDGK..M.D.KV
Retrocopy EILKMFLKEENEHH<HRHSSHYASERLPSKKHQEEG>VMEKLHNGDLDHMTPQHCNSELDGKRSMIDGKV

Parental  IVGSLSVQDLQASQSACYW-LKGVRYSDIGTLAWMITLSDGLHNFIDGLAIGASFTVSVFQGIST-SVAI
          .VGSLSV..LQA.QSAC...LKGV.Y..I.TLAW.I.LS..LHN....LAIGASFT..V.QG..T..VAI
Retrocopy VVGSLSVLVLQAPQSACWS<LKGVHYF-ISTLAWVIALSSSLHNVLSSLAIGASFTMCVVQGLGT<LVAI

Parental  LCEEFPHELGDFVILLNAGMSIQQALFFNFLSACCCYLGLAFGILAGSHFSANWIFALAGGMFLYISLAD
          ..EEFPH...DFVILL.AG..IQ..L........CCY.GLAFGILA.SHFSA.WIF.L.GGMFL....AD
Retrocopy FHEEFPH---DFVILLSAGRTIQHCLLQT--PSTCCYVGLAFGILASSHFSASWIFVLVGGMFLNTAVAD

Parental  MFPEMNEVCQEDERKGSILIPFVIQNLGLLTGFTIMVVLTMYSGQIQIG
          MFPE.NEVCQ.D..KGS..IPFVIQNLGLL..FT.M.VL...SGQIQIG
Retrocopy MFPETNEVCQDDGGKGSNSIPFVIQNLGLLARFTVMLVLMVCSGQIQIG

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_1765 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018834	1 retrocopy	retro_dnov_1567,
Homo sapiens	ENSG00000104635	1 retrocopy	retro_hsap_322,
Gorilla gorilla	ENSGGOG00000003765	1 retrocopy	retro_ggor_348,
Nomascus leucogenys	ENSNLEG00000015557	1 retrocopy	retro_nleu_1765 ,