RetrogeneDB ID: retro_nleu_1634

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397302.1:12010800..12012296(+)
• 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_1634
ATGTCTACCAACGAGAATGCTAACATAGCAGTTGCCCGACTTCACAGATTCAAGAACAAGTGAAAAGACAGTACAGAAAT
GAGGTGTTGCAGAATAGAAGTCAATGCGAAGCTGAGGAAAACTAAGAAGAATGACCAGATGCTGAAGAGGAGAAATGCAA
GCTCATTTCCTGATGTTGCTGCTTCTCCGCTGGAGAAAAACCGCAAAAACCAGGGCACTGTAAATTGGTCTGTTGATGAC
ATTGTCAAAGGCACAAATAGCAACAATGTGGAAAGTCAGCTCCAAGCTACTCAAGCTGCCATGAAACTACTTTCTAGAGA
AAAACAGCCCCCCATAGGCAACATAATCTGGGCTGGTTTGATTCCAAAATTTGTGTCCTTCTTGGGCAGAACTGATTGTA
GTCCCATTCAGTTTGAATCCGCTTGGGCACTTACTAACATTGCTTCTGGGACATCAGAATAAACCAAGGCTGTGGTAGAT
GGAGGTGCCATCCCAGCATTCATTTCTCTGTTAGCATCTCCCCATGCTCACATCAGTGAACAAGCTGTATGGACTCTAGG
AAACATTGCAGGTGATGGTTTAGTTTTCCGAGACTTGGTTATTAAGTATGGTGCAGTTGACCCACTCTTGGCTCTTCTTG
CAGTTCTCGATATGTCATCTTTAGTATGTGGTTACTTATGTCATCTTACCTGGACACTTTCAATCCTCTGCTGCTACAAG
AATCCTGCACCCCCGTTAGATGCTATTGAGCAAATTCTTCCTACCTTAGTTTGACTCATGCATCATGATGATCCAGAAGT
ATTAGCAGATAGCTGTTGGGCTATTTCCTACCTTACTGATGGTCCAACTAAACGAATTGACATGTCCTTGAAAACAGGAG
TTCTGCCCCAACTTGTGAAGCTTCTAGGAACTTCTGAATTGCCAACTGTGACTCCTGCACTAAGACCCATAGGGAATATT
GTCACTGGTACAGATGAAGAGACTCAGGTTGTGATCGACGCAGGAGCACTTGCTGTCTTTCCCACCCTGCTCATCAACCC
CAAAACTAACTTTCAGAAGGAAGCTACATGAACAATGTCAAATGTCACAGCTGACCTTCAGGACGAGACACAGCAAGTTG
TGAATCATGGATTAGTCCCATTCCTCACAACGTTCTCTCTAAGGCAGATTTTAAGACACAAAAGGAAGCTGTATGGGCCA
TGAACAACTATACCAGTGGTGGAACATTTGAACAGGCTGTATACCTCATTCATTGTGGCATAATAAAACCATTGATGAAC
CTCTTAACTTCAAAAGATACCAAGATTATTCTGGCTATCCTGGATGCCGTTCCGAACATCTTTCAGGCTGCTGAGAAACT
AGGTGAAACTGAGAAACTTAGTACAATGATTGAAGAATGTGGAGGCTTAGACAAAATTGGAGCTCTACAAAACCATGAAA
ATGAGTCTGTGTATAAGGCTTTGTTAAGCTTAATTGAGAAGAATTTCTCGGTAGAG

Alignment

ORF - retro_nleu_1634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.2 %
• Parental protein coverage: 99.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTNENANTPAARLHRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
          MSTNENAN...ARLHRFKNK.KDSTEMR..RIEVN..LRK.KK.DQMLKRRN.SSFPD.A.SPL..NR.N
Retrocopy MSTNENANIAVARLHRFKNK*KDSTEMRCCRIEVNAKLRKTKKNDQMLKRRNASSFPDVAASPLEKNRKN

Parental  QGTVNWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFES
          QGTVNWSVDDIVKG.NS.NVE.QLQATQAA.KLLSREKQPPI.NII.AGLIPKFVSFLGRTDCSPIQFES
Retrocopy QGTVNWSVDDIVKGTNSNNVESQLQATQAAMKLLSREKQPPIGNIIWAGLIPKFVSFLGRTDCSPIQFES

Parental  AWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLL
          AWALTNIASGTSE.TKAVVDGGAIPAFISLLASPHAHISEQAVW.LGNIAGDG.VFRDLVIKYGAVDPLL
Retrocopy AWALTNIASGTSE*TKAVVDGGAIPAFISLLASPHAHISEQAVWTLGNIAGDGLVFRDLVIKYGAVDPLL

Parental  ALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPVPPIDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTD
          ALLAV.DMSSL.CGYL..LTWTLS.LC..KNP.PP.DA.EQILPTLV.L.HHDDPEVLAD.CWAISYLTD
Retrocopy ALLAVLDMSSLVCGYLCHLTWTLSILCCYKNPAPPLDAIEQILPTLV*LMHHDDPEVLADSCWAISYLTD

Parental  GPNERIDMVVKTGVVPQLVKLLGASELPIVTPALKAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTN
          GP..RIDM..KTGV.PQLVKLLG.SELP.VTPAL..IGNIVTGTDE.TQVVIDAGALAVFP.LL.NPKTN
Retrocopy GPTKRIDMSLKTGVLPQLVKLLGTSELPTVTPALRPIGNIVTGTDEETQVVIDAGALAVFPTLLINPKTN

Parental  IQKEATWTMSNITAGRQDQIQQVVNHGLVPFLV-SVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHC
          .QKEAT.TMSN.TA..QD..QQVVNHGLVPFL...VLSKADFKTQKEAVWA..NYTSGGT.EQ.VYL.HC
Retrocopy FQKEAT*TMSNVTADLQDETQQVVNHGLVPFLT<NVLSKADFKTQKEAVWAMNNYTSGGTFEQAVYLIHC

Parental  GIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASL
          GII.PLMNLLT.KDTKIIL.ILDA..NIFQAAEKLGETEKLS.MIEECGGLDKI.ALQNHENESVYKA.L
Retrocopy GIIKPLMNLLTSKDTKIILAILDAVPNIFQAAEKLGETEKLSTMIEECGGLDKIGALQNHENESVYKALL

Parental  SLIEKYFSVE
          SLIEK.FSVE
Retrocopy SLIEKNFSVE

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_1634 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,