RetrogeneDB ID: retro_nleu_973

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397277.1:26723873..26725236(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSNLEG00000003486
• Aliases: None
• Description: None

Sequence

>retro_nleu_973
GTGGAAACTGAACAGCCAGAAGAAACCTTCCCTAACACTGAAACCAATAGTGAATTTGGTAAATGCCCTGCAGAAGATAT
GGAAGAGGAACAAGCGTTGAAAAGATCTAGAAACACTGATGAGATGGTTGAATTACACATTCTGCTTCAGAACAAGAATG
CTGGGGCAGTGATTGGAGAAGGAGGCAAGAATATTAAGGCTCCCTGTGTAGACTACAATGCCAGTGTTTCGGTCCCAGAC
AGCAGTGGCCCCGAGTGCATACTGAGTATCAGTGCTGATATTGAAACAATTGGAGAAATTCTAAAGAAAATCATCCCTAC
CTTGGAAGAGGCCCTGCAGTTGCCATTACTCACTGCAACCAGCCAGCTCCTGCTGGAATCTGATGCTGTGGAATGCTTAA
ATTACCAACGCTATAAAGGAAGAGACTTTGGGTGCAAGTTGAAGCAGTTGATTCATCAGAGTCTAGCAGGAGGAATATTG
GGGTCAAAGGTGCTAAAATCAAAGAACTTTGAGAGAACACTCAAACAACCATCAAGCTTTTCTAGGAATGCTGTTCTCAT
CCCACTGACAGAGTTGTTCTTATTGGAGGAAAACCCAATAGGGTTGTAGAGTGCATAAAGATCATCCTTGATCTTATATC
TGAGTCTCCCATCAAAGGACCTGCACAGCCTTATGATCCCAGTTTTTACAATGAAACCTATGATTATGGTGGTTTTACGA
TGATGTTTGATGACTGCCCTGGAAGCCCAGTGGGATTTCCGATGTGGGGAAGAGGTGGTTTTGACAGAATGCCTCCTGGT
TGGGGTGGGCGTCCCATGCTTCCATCTAGAAGAGATATGAGCCCTCATCGAGGACCACCTTCTCCTACTACTGGACAAGG
TGGCTGGGGTGGTAGCAGAGCTTGGAATCTTCCTCTTCACCACCACCACCTAGAGGGGGAGACCTAATGGCCTATGACAG
AAGAGGGAGACCTGGAGACTGTTATGATGGCATGGTTGGTTTCAGTCCTGATGAAACTTGGAACTCTGCAATAGATACAT
GGAGCCCATCAGAATGGCAGATGGCTTATGAACCACAGGGTGGCTCCGGATATGATTATTCCTATGCAGGGGTTGGTGGC
TCATATGGTGATCTTGGTGGACCTATTATTACTGCACAAGTAACTATTCCCAAAGATTTGACTGGATCTATTATTGGCAA
AGATGGTCAGCGGATTAAACAAATTGGTCATGAGTTGGGAGCTTCAATCAAAATTGATGAGCCTTTAGAAGGATCCGAAG
ATCGGATCATTACCATTACAGGAACACAGGACCAGATACAGAATGCACAATATTTGCTGCAGAACAATGTGAAGCAGTAT
TCT

Alignment

ORF - retro_nleu_973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.68 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  METEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRT
          .ETEQPEETFPNTETN.EFGK.PAEDMEEEQA.KRSRNTDEMVEL.ILLQ.KNAGAVIG.GGKNIKA...
Retrocopy VETEQPEETFPNTETNSEFGKCPAEDMEEEQALKRSRNTDEMVELHILLQNKNAGAVIGEGGKNIKAPCV

Parental  DYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG
          DYNASVSVPDSSGPE.ILSISADIETIGEILKKIIPTLEE.LQLP..TATSQL.LESDAVECLNYQ.YKG
Retrocopy DYNASVSVPDSSGPECILSISADIETIGEILKKIIPTLEEALQLPLLTATSQLLLESDAVECLNYQRYKG

Parental  SDFDCELRLLIHQSLAGGI-IGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKII
          .DF.C.L..LIHQSLAGGI.IGVKGAKIKEL.ENTQTTIKLF.ECC.H.TDRVVLIGGKP.RVVECIKII
Retrocopy RDFGCKLKQLIHQSLAGGI<IGVKGAKIKEL*ENTQTTIKLF*ECCSHPTDRVVLIGGKPNRVVECIKII

Parental  LDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRD
          LDLISESPIKG.AQPYDP.FY.ETYDYGGFTMMFDD..G.PVGFPM.GRGGFDRMPPG.GGRPM.PSRRD
Retrocopy LDLISESPIKGPAQPYDPSFYNETYDYGGFTMMFDDCPGSPVGFPMWGRGGFDRMPPGWGGRPMLPSRRD

Parental  YDDMSPRRGPPPPPPGRGGRGGSRARNLPL-PPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSA
          ...MSP.RGPP.P..G.GG.GGSRA.NLPL..PP.PPRGGDLMAYDRRGRPGD.YDGMVGFS.DETW.SA
Retrocopy ---MSPHRGPPSPTTGQGGWGGSRAWNLPL<SPP-PPRGGDLMAYDRRGRPGDCYDGMVGFSPDETWNSA

Parental  IDTWSPSEWQMAYEPQVEYHTDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESG
          IDTWSPSEWQMAYEPQ.....DYSYAG..GSYGDLGGPIIT.QVTIPKDL.GSIIGK.GQRIKQI.HE.G
Retrocopy IDTWSPSEWQMAYEPQGGSGYDYSYAGVGGSYGDLGGPIITAQVTIPKDLTGSIIGKDGQRIKQIGHELG

Parental  ASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYA
          ASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQN.VKQY.
Retrocopy ASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNNVKQYS

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_973 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 16 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Nomascus leucogenys	ENSNLEG00000002639	1 retrocopy	retro_nleu_2044,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973 ,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Tarsius syrichta	ENSTSYG00000001196	3 retrocopies	retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,