RetrogeneDB ID: retro_nleu_1714

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:5811047..5811900(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AZI2
• Ensembl ID: ENSNLEG00000004069
• Aliases: None
• Description: None

Sequence

>retro_nleu_1714
TGCATTAATAGAGATGATTTAAAGAGCAAATTGGATAAAATAAGTAAACACAACTCTGAATCTTTAAAAGTATTGAATAA
ACAGATGCAATCTAAAGAAGTAGAACTCTAGCTAAGGACAGAGGTGGAAACTCAACTGGTGATGAGGAATTTCAATCCAC
CTTCATCAAACTGGGAGGTGGAAAAGTTAAGCTGTAACCTGAAGATCCATGGTTTGGAACAAGAGTTGATGAGGAAAGAA
TGTAAGGATCTCAAAATAGAACTACTCAAAAACCAAACAAACCTATCTGTATCAGGAAGACAATCTTGAAGGGCAGAGAT
CTCTGAAGAGTAAGAACTTCAAGTGATAATACGCAGAACGTATACTGGCAACTGAAGAGATAAATGTCTAATTTATATCT
GGTGACTCAAGTGCTAGCTGAACTATTAAGAAAACTGGAAACCCCAACTGCAATCAAGAAAGCCTGCACCTCAGTAGGAT
GCATTGAAGACCCTTGGAAAGACGGCACAAAACTGCACATGATGAATTTTACTGCAACATACAGAACACATCCCCTTCTC
TCACCAAATGGCAAAGCTCTTTGTTATACTACATCTTCCCCTTTACCAGGAGATATAAAGGTTTTATCAGAGAAAGCAGT
CCTCCAATCACGGACAGATAATGAGAGAGCCATTCCTAATGAGGGCAGACACTCTTATGGCAGAAATTCTCTGGAAGATC
ATTTTGAGTATTCCCAATCCGTCCTGACTCAAGTGAGACAGCATTTAGGTAAATTAAAGTAAAATTTTGCATTCTAACCA
GTGTGCCATTACTGCATTACTTGGATCAACATAATCAAAATTTCCTTTATAAG

Alignment

ORF - retro_nleu_1714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.9 %
• Parental protein coverage: 74.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CIDRDNLKSKLDKMNKDNSESLKVLNEQLQSKEVELLQLRTEVETQQVMRNLNPPSSNWEVEKLSCDLKI
          CI.RD.LKSKLDK..K.NSESLKVLN.Q.QSKEVEL..LRTEVETQ.VMRN.NPPSSNWEVEKLSC.LKI
Retrocopy CINRDDLKSKLDKISKHNSESLKVLNKQMQSKEVEL*-LRTEVETQLVMRNFNPPSSNWEVEKLSCNLKI

Parental  HGLEQELELMRKECSDLKIEL-QKAKQTDLYQEDNL-KSRDLQKLSISSDNMQHAYWELKREMSNLHLVT
          HGLEQEL..MRKEC.DLKIEL..K.KQT.LYQEDNL.K.RDL.....SSDN.Q..YW.LKR.MSNL.LVT
Retrocopy HGLEQEL--MRKECKDLKIEL>SKTKQTYLYQEDNL>KGRDL*RVRTSSDNTQNVYWQLKR*MSNLYLVT

Parental  QVQAELLRKLKTSTAIKKACAPVGCSEDLGRDSTKLHLMNFTATYTRHPPLSPNGKALCHTASSPLPGDV
          QV.AELLRKL.T.TAIKKAC..VGC.ED...D.TKLH.MNFTATY..HP.LSPNGKALC.T.SSPLPGD.
Retrocopy QVLAELLRKLETPTAIKKACTSVGCIEDPWKDGTKLHMMNFTATYRTHPLLSPNGKALCYTTSSPLPGDI

Parental  KVLSEKAVLQSWTDNERSIPNDGTCFQEHSSYGRNSLEDNSW-VFPSPPKSSETAFGETKTKTLPLPNLP
          KVLSEKAVLQS.TDNER.IPN.G.....HS.YGRNSLED....VFP..P.SSETAF...K.K...L...P
Retrocopy KVLSEKAVLQSRTDNERAIPNEG----RHS-YGRNSLEDHFE<VFPIRPDSSETAFR*IKVKFCILTSVP

Parental  PLHYLDQHNQNCLYK
          .LHYLDQHNQN.LYK
Retrocopy LLHYLDQHNQNFLYK

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_1714 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010432	2 retrocopies	retro_chof_1794, retro_chof_234,
Dasypus novemcinctus	ENSDNOG00000011053	2 retrocopies	retro_dnov_1377, retro_dnov_542,
Homo sapiens	ENSG00000163512	2 retrocopies	retro_hsap_1491, retro_hsap_1564,
Gorilla gorilla	ENSGGOG00000022881	2 retrocopies	retro_ggor_1145, retro_ggor_1189,
Loxodonta africana	ENSLAFG00000008538	2 retrocopies	retro_lafr_529, retro_lafr_925,
Myotis lucifugus	ENSMLUG00000000043	3 retrocopies	retro_mluc_1707, retro_mluc_435, retro_mluc_611,
Macaca mulatta	ENSMMUG00000000056	1 retrocopy	retro_mmul_2135,
Monodelphis domestica	ENSMODG00000015075	1 retrocopy	retro_mdom_1786,
Nomascus leucogenys	ENSNLEG00000004069	1 retrocopy	retro_nleu_1714 ,
Oryctolagus cuniculus	ENSOCUG00000014956	1 retrocopy	retro_ocun_1778,
Otolemur garnettii	ENSOGAG00000005896	1 retrocopy	retro_ogar_3078,
Pongo abelii	ENSPPYG00000014053	2 retrocopies	retro_pabe_1241, retro_pabe_3784,
Pan troglodytes	ENSPTRG00000014707	1 retrocopy	retro_ptro_1052,
Tursiops truncatus	ENSTTRG00000016434	1 retrocopy	retro_ttru_1093,