RetrogeneDB ID: retro_nleu_2431

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397354.1:4371674..4372450(-)
• Located in intron of: ENSNLEG00000000350

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF3
• Ensembl ID: ENSNLEG00000017046
• Aliases: None
• Description: None

Sequence

>retro_nleu_2431
ATGCTCATGTTTGACCCAGTTCCTGTTAAGCAAGAGGCCCATGGACCCTGTCTCAGTGTCATACTCATCTAATTACATGG
AATCCATGAAGCCGACAAGTATGGGGTCATCTACTCCACACAATTGCCTGATAAGTTCTTTCAGACCCTAGAAGGCCTGT
TGCACGAAATACAGATGGAGCCAATGGACTTCATGGTGAGCAAGCAGAGTTCACCTCCTTCTGCTGGGAATTCGCACTCC
TCTCTGAAGTTCCTATCCTCACACCAGAGAGCCTCGCCTGGGTTGAGCCTGCCTTCTTCCAGCCCACCAATGAAAGTACT
CATCCCCTTCTCCAGGCTAGCAACCCTTTGATATGCCACTTGTCCATGCCGCGGGTGATGGCAGCTGCCCTCTCCTGGCA
CAGAATACGGAGCCTGGGGATCTTGCTGGTCATCCAGCCGTTGGTGGTGCAGCCATCCCCCTTATGTACATGAGTCACCT
GGAGCAGCCTCTCATGGTCTCCTTAAGGAGGAAGAGGTCATCCATGAAAGAGATGAAAAATTCCAGTAGTAGCATACAAG
TACCTGTTATTGAATCACAAGAAAATCCTGTATCAGAGAAAAAAATTAAAATAGAACCTGGGATCGAACCACAGAGGACG
GATTATCCTGAAGAAATGTCACCCCCCCTTAATGAACTCAGCGTCCCCCCCGCAAGCATTGTTGCAAGAGAATCACCCTT
TGGTCATCGTGCAGCCTGGGAAGAGAACTTTACCTGTGGAATCCCCGGATACTCGA

Alignment

ORF - retro_nleu_2431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.56 %
• Parental protein coverage: 73.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MLMFDPVPVKQEA-MDPISVSYPSNYMESMKP-NKYGVIYSTPLPEKFFQTPEGLSHGIQMEPVDLTVNK
          MLMFDPVPVKQEA.MDP.SVSY.SNYMESMKP..KYGVIYST.LP.KFFQT.EGL.H.IQMEP.D..V.K
Retrocopy MLMFDPVPVKQEA>MDPVSVSYSSNYMESMKP<DKYGVIYSTQLPDKFFQTLEGLLHEIQMEPMDFMVSK

Parental  RSSPPSAGNSPSSLKFPSSHRRASPGLSMPSSSPPIKK-YSPPSPGVQPFGVPL-SMPPVMAAALSRHGI
          .SSPPSAGNS.SSLKF.SSH.RASPGLS.P.SS.P..K.YS.PSPG.QPF..PL.SMP.VMAAALS.H.I
Retrocopy QSSPPSAGNSHSSLKFLSSHQRASPGLSLP-SSSPPMK>YSSPSPG*QPFDMPL>SMPRVMAAALSWHRI

Parental  RSPGILPVIQPVVVQP-VPFMYTSHLQQPLMVSL----SEEMENSSSSMQV--PVIESYEKPISQKKIKI
          RS.GIL.VIQP.VVQP..P.MY.SHL.QPLMVSL....S...E...SS.....PVIES.E.P.S.KKIKI
Retrocopy RSLGILLVIQPLVVQP<IPLMYMSHLEQPLMVSLRRKRSSMKEMKNSSSSIQVPVIESQENPVSEKKIKI

Parental  EPGIEPQRTDYYPEEMS-PPLMNSVSPPQALLQENHPSVIVQPGKRPLPVESPDTQ
          EPGIEPQRTD.YPEEMS.PPLMNS.SPPQALLQENHP.VIVQPGKR.LPVESPDT.
Retrocopy EPGIEPQRTD-YPEEMS>PPLMNSASPPQALLQENHPLVIVQPGKRTLPVESPDTR

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_2431 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017488	1 retrocopy	retro_btau_271,
Choloepus hoffmanni	ENSCHOG00000004256	1 retrocopy	retro_chof_181,
Macaca mulatta	ENSMMUG00000003363	1 retrocopy	retro_mmul_2118,
Nomascus leucogenys	ENSNLEG00000007123	1 retrocopy	retro_nleu_620,
Nomascus leucogenys	ENSNLEG00000016120	1 retrocopy	retro_nleu_65,
Nomascus leucogenys	ENSNLEG00000017046	1 retrocopy	retro_nleu_2431 ,
Otolemur garnettii	ENSOGAG00000006524	1 retrocopy	retro_ogar_1686,