RetrogeneDB ID: retro_nleu_1726

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:3776624..3777793(-)
• Located in intron of: ENSNLEG00000004576

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT75
• Ensembl ID: ENSNLEG00000017753
• Aliases: None
• Description: None

Sequence

>retro_nleu_1726
AGTGGAGGAATCACTGCTGTCACTGTCAACCAAAGCCTGCTGAGCCCTCTTAACCTGGAGGTGGACCTCAACATCCAGGC
GGTGCGCACCCAGGAGGAGAAGCAGATCAAGACCCTCAACAACAAGTTTGCCTCTTTCATAGACAAGGTACGGTTCCTGG
AGCAGCAGAACAAGATGCTGGAGACCAAGTGGAGCCTTGTGCAGCAGCAAAAGATGGCTCGGAGCAACATGGACAACATG
TTCGAGAGCTACATCAACAGCCTTAGGTGGCAGCGGAGACTCTGGGCCAGGAGAAACTGAAGCTGGAGGCGGAGCTTGGC
AGCATGCACAGGCTGGTGGAGGACTTCAGGAACAAGTATGAGGATGAGATCAGTATGTGTACAGAGATGGAGAATGAATT
TGTGCTCATCAACGGAGGATGTGGGTGAAGCTTACATGAACAAGATGGAGCTGAGTCTCCCCTGAAGGGCTGACTGCCGA
GATCAGCTTCTTCAGGCAGCTGTATGAAGAGGAGATCAGGAGCTGCAGTACCAGATCTCGGATACATCTGTGGTGCTGTT
CATGGACAACAGCCGCTTCCTGGACATGGGCAGCATCATCCCTGAGGTCAAGAGGCAGTACGAGGAGATTGCCAACCGCA
GCCGGGCTGAGGCTGAGAGCATGTACTAGATTAAGTATAAGGAGCTGCAGACGCTGGGTCGGAAGCATGGGGATGACCTG
TGGCGTGCAAAGACTGAGATCTCCTAGATGAACCGGAACATCAGCGGGCTCCAAGCTGAGACTGAGGGTCTTAAAGGCCA
GCGGGCTTCCCTGGAGGCCGCCACGCAGATACCAAGCAGCGTGGGGAGCTGGCCATTAAGGATGCCGACGCCAAGCTGTC
TGAGCTGGAGGCTGCCCTGCAGCTAGCCAGTCAAGACATGGCGCAGCAGCTGCATGAGTACCAGGAGCTGATGAAGGTCA
AGCTGGCCCTGGATATCAAGATCGCCACCTACAGGAAGCTGTTGGAGGGTGAGGAGAGCTGGCTGGAGTCTGGGATGCAG
AACATGAGTATCCATATGAAGACCACCAGCAGCTATGCAGGTGGTCAGAGCTTGGCCTATGGGGGCCTCACAAGCCCTGG
CCTCAGCTAAGGCCTGGGCTCCAGCTTTGGCTCTGGCATGGGCTCCAGC

Alignment

ORF - retro_nleu_1726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.58 %
• Parental protein coverage: 65.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AGGIQEVTVNQSLLTPLNLQIDPTIQRVRAEEREQIKTLNNKFAAFIDKVRFLEQQNKVLETKWALLQEQ
          .GGI..VTVNQSLL.PLNL..D..IQ.VR..E..QIKTLNNKFA.FIDKVRFLEQQNK.LETKW.L.Q.Q
Retrocopy SGGITAVTVNQSLLSPLNLEVDLNIQAVRTQEEKQIKTLNNKFASFIDKVRFLEQQNKMLETKWSLVQQQ

Parental  GSRTVRQNLEPLFDSYISEFRRQ-LESVTTERGRLEAELRNMQDVVEDFKIRYEDEINKRTAAENEFVAL
          .....R.N....F.SYI...R.Q..E....E...LEAEL..M...VEDF...YEDEI...T..ENEFV..
Retrocopy --KMARSNMDNMFESYINSLRWQ<AETLGQEKLKLEAELGSMHRLVEDFRNKYEDEISMCTEMENEFVLI

Parental  K-KDVDAAYMNKVEL-EAKVKS-LPEEINFLHSVFDAEL-SQLQTQVSDTSVVLSMDNNRNLDLDSIIAE
          ...DV..AYMNK.EL.E...K..L..EI.F.......E....LQ.Q.SDTSVVL.MDN.R.LD..SII.E
Retrocopy N>EDVGEAYMNKMEL<ESPLKG<LTAEISFFRQLYEEEI<QELQYQISDTSVVLFMDNSRFLDMGSIIPE

Parental  VKAQYEDIANRSRAEAESWYQTKYEELQVTAGRHGDDLRNTKQEISEMNRMIQRLRAEIDSVKKQCSSLQ
          VK.QYE.IANRSRAEAES.Y..KY.ELQ.....HGDDL...K.EIS.MNR.I..L.AE....K.Q..SL.
Retrocopy VKRQYEEIANRSRAEAESMY*IKYKELQTLGRKHGDDLWRAKTEIS*MNRNISGLQAETEGLKGQRASLE

Parental  TAI-ADAEQRGELALKDARAKLVDLEEALQKAKQDMARLLREYQELMNIKLALDVEIATYRKLLEGEECR
          .A..AD..QRGELA.KDA.AKL..LE.ALQ.A.QDMA..L.EYQELM..KLALD..IATYRKLLEGEE..
Retrocopy AAT<ADTKQRGELAIKDADAKLSELEAALQLASQDMAQQLHEYQELMKVKLALDIKIATYRKLLEGEESW

Parental  LSGEGVSPVNISVVTSTLSSGYGSGSSIGGGSL---GLGGGSGYSFTTSGGHS
          L...G.....I...T....S.Y..G.S...G.L...GL..G.G.SF....G.S
Retrocopy LE-SGMQNMSIHMKT---TSSYAGGQSLAYGGLTSPGLS*GLGSSFGSGMGSS

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_1726 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 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003743	10 retrocopies	retro_chof_1530, retro_chof_1645, retro_chof_2414, retro_chof_2471, retro_chof_2544, retro_chof_2704, retro_chof_322, retro_chof_693, retro_chof_750, retro_chof_915,
Microcebus murinus	ENSMICG00000002186	1 retrocopy	retro_mmur_747,
Nomascus leucogenys	ENSNLEG00000017733	8 retrocopies	retro_nleu_1913, retro_nleu_225, retro_nleu_2285, retro_nleu_2421, retro_nleu_2485, retro_nleu_2727, retro_nleu_2787, retro_nleu_672,
Nomascus leucogenys	ENSNLEG00000017740	1 retrocopy	retro_nleu_1808,
Nomascus leucogenys	ENSNLEG00000017746	5 retrocopies	retro_nleu_2270, retro_nleu_2596, retro_nleu_354, retro_nleu_457, retro_nleu_852,
Nomascus leucogenys	ENSNLEG00000017748	2 retrocopies	retro_nleu_2823, retro_nleu_3100,
Nomascus leucogenys	ENSNLEG00000017753	1 retrocopy	retro_nleu_1726 ,
Nomascus leucogenys	ENSNLEG00000017758	2 retrocopies	retro_nleu_593, retro_nleu_726,
Nomascus leucogenys	ENSNLEG00000026579	1 retrocopy	retro_nleu_311,