RetrogeneDB ID: retro_nleu_208

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:19606959..19607866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA2
• Ensembl ID: ENSNLEG00000001749
• Aliases: None
• Description: Importin subunit alpha [Source:UniProtKB/TrEMBL;Acc:G1QMK1]

Sequence

>retro_nleu_208
CTAAGAAGGAGAAATGTAAGCTCATTTCCTGATGATGCTACTTCTCCACTGCAGAAGAACTGTAACAACCAGGATACTGT
AAATCGGTCTGTTGATGACATTGTCAAAGGTATAAATAACAACAATGTGGAAAGTCAGCTGTAAGCTACTCAAGCTGCCA
GGAAACTACCTTCTGGAGAAAACCAGCCCCCCATAGACAACATAATCCAGGCTGGTTTGCTTCCAACATTTCCATCCTTC
TTGGGAAGAACTAATTGTAGTCCCATTCAGTTTGAATCTGCTTGGGCACTCACTAACATTGCTTCTGGGGCATCAGAACA
GACCAAGGCTGTGGTAGACGGAGGTGCCATCCCAGCATTCATTTCTCTGCTGGCATCTCCCCATGCTCACATCAGTGAAC
GAGCTGTATGGGCTCTAGGAAACGTTGCAGGTGATGGTTCCATTTTCCGAGACTTGGTTATCAACTGCGGTGCAGTTGAC
CCACTGTTGGCTCTTCTTGCAGTTCCTGATATGTCATCTTTAGCATGCGGTTACTTAAGTAATCTTACGTGGACACTTTC
AAACCTTTGCCACAAGAATACTCGCACCTCCTTTAGATTCTGTTGAGCAAATTTTTCCTACGTTAGTTTGATTCCTGCAT
CAGGATGATCCAGAAATATTAGCAGATATCTGCTGGGTTATTCCTTACCTTTCTGGTGGTCCAAATGAATGAAGTGACAT
GGTCGTGAAAACGGGAGTTTTGCCCCAACTTGTGAAGTCTCTAGGAGCTTCTGAATTGCCATTTGTGACTCCAGCACTAA
GAGCCATTGGGAATATTGTCACTGGTACAGATGAACAGACTCAGGTTGTGATTGATGCAGGAGCACTCACCATCTTTCCC
AGCCTGCTAATCAACCCCAAAACTAAC

Alignment

ORF - retro_nleu_208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.55 %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKRRNVSSFPDDATSPLQENRNNQGTVNWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIR
          L.RRNVSSFPDDATSPLQ.N.NNQ.TVN.SVDDIVKGIN..NVE.QL.ATQAARKL.S.E.QPPIDNII.
Retrocopy LRRRNVSSFPDDATSPLQKNCNNQDTVNRSVDDIVKGINNNNVESQL*ATQAARKLPSGENQPPIDNIIQ

Parental  AGLIPKFVSFLGRTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALG
          AGL.P.F.SFLGRT.CSPIQFESAWALTNIASG.SEQTKAVVDGGAIPAFISLLASPHAHISE.AVWALG
Retrocopy AGLLPTFPSFLGRTNCSPIQFESAWALTNIASGASEQTKAVVDGGAIPAFISLLASPHAHISERAVWALG

Parental  NIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNP-VPPIDAVEQILPTL
          N.AGDGS.FRDLVI..GAVDPLLALLAVPDMSSLACGYL.NLTWTLSNLC..KN...PP.D.VEQI.PTL
Retrocopy NVAGDGSIFRDLVINCGAVDPLLALLAVPDMSSLACGYLSNLTWTLSNLC-HKNT>APPLDSVEQIFPTL

Parental  VRLLHHDDPEVLADTCWAISYLTDGPNERIDMVVKTGVVPQLVKLLGASELPIVTPALKAIGNIVTGTDE
          V..LH.DDPE.LAD.CW.I.YL..GPNE..DMVVKTGV.PQLVK.LGASELP.VTPAL.AIGNIVTGTDE
Retrocopy V*FLHQDDPEILADICWVIPYLSGGPNE*SDMVVKTGVLPQLVKSLGASELPFVTPALRAIGNIVTGTDE

Parental  QTQVVIDAGALAVFPSLLTNPKTN
          QTQVVIDAGAL..FPSLL.NPKTN
Retrocopy QTQVVIDAGALTIFPSLLINPKTN

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_208 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 20 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018411	3 retrocopies	retro_amel_1161, retro_amel_1318, retro_amel_440,
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Cavia porcellus	ENSCPOG00000026318	1 retrocopy	retro_cpor_46,
Dasypus novemcinctus	ENSDNOG00000019151	6 retrocopies	retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Felis catus	ENSFCAG00000001936	2 retrocopies	retro_fcat_1176, retro_fcat_921,
Homo sapiens	ENSG00000182481	1 retrocopy	retro_hsap_2950,
Gorilla gorilla	ENSGGOG00000027535	2 retrocopies	retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus	ENSMLUG00000027946	7 retrocopies	retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta	ENSMMUG00000018256	3 retrocopies	retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Nomascus leucogenys	ENSNLEG00000001749	3 retrocopies	retro_nleu_1052, retro_nleu_1634, retro_nleu_208 ,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680,
Otolemur garnettii	ENSOGAG00000027672	7 retrocopies	retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii	ENSPPYG00000008569	1 retrocopy	retro_pabe_3501,
Pteropus vampyrus	ENSPVAG00000004976	2 retrocopies	retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Sarcophilus harrisii	ENSSHAG00000011391	1 retrocopy	retro_shar_165,
Vicugna pacos	ENSVPAG00000001855	3 retrocopies	retro_vpac_124, retro_vpac_162, retro_vpac_163,