RetrogeneDB ID: retro_nleu_1815

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397311.1:3838723..3839870(-)
• 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_1815
ATGGAAACTGAACAGCCAGAAGAAACCTTCCCTAACACTGAAACCAGTGGTGAATTTGGTAAACACCCTGCAGAAGATAT
AGCAGAGGAACAAGCATTTAAAAGATCTAGAAATACTGATGAGATGGTTGAATTAGCCATTCTGCTTCAGAGCAAGAATG
CTGGGGCAGTGACTGGAAAAGGAGGCAAGAATATTAAGGCTTTCCGTACAGACTACAACACCAGCGTTTCAGTTCTAGAC
AGCAGTGGCCCCGAGCGCATATTGCGTATCAGTGCTCATATCAAAACAATTGGAGAAATTCTGAAGAAAATCATCCCTAC
CTTGGAAGAGGGCCTGCAGTTGCCATCACCCACTGCAACCAGCCAGCTCCCGCTCGAATCTGATGCTGTGGAATACTTAA
ATTACCAACACTATAAAGCAAGGGACTTTGACTGCGAGTTGAAGCTGTTGATTCATCAGAGTCTAGCAGGAGGAATTATT
GGGGTCAAAGGTGCTAAACTCAAAGAACTGAGAAAACACACAAACAACCATCACGCTTTTCCAGGAATGTTGTCCTCATT
TCACTGATAGAGTTGTTCTTATTGGAGGAAAACCCAATAGGGTTGTAGAGTGCATAAAGATCATCCTTGATCTTATTTAT
GAGTCTCCCATCAAAGGACATGCACAGCCTTATGATCCCAATTTTTACAATGAAACCTATGATTATGATGGTTTTACAAT
GGTGTTTGCTGACCACCGTGGACGCCCAGTGAGATTTCTGATGCGGGGAAGAGGTGGTTTTGACAAAATGTCTCCTGGTC
GGGGTGGGCGTCCCATGCCTCCATCTAGAAGAGATTATGTTTATATGAGCCCTCGTCAAGGACCACCTCCCCTTCCTCCC
AGATGAGGTGGCCAGAGTGGTAGCAAAGCTCAGAATGCTCCTCTTCCTCCACCACCACCACCTAGAGGGGGAGACCTCAT
GACCTATAACAGAAAAGGGAGACCTGGAGACCGTTACAACGGCGTGGTTGATTTCAGTGCTGATGAAACTTGGGACTCTG
CAATAGATACATGGAATGCATCAGAATGGCAGATGGCTTATGAACCACAGGGTGGCTCCAGATATGATTATTCCTATGCA
GGGGGTCATGGCTCATATGGTGATCTT

Alignment

ORF - retro_nleu_1815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.81 %
• Parental protein coverage: 82.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  METEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRT
          METEQPEETFPNTET.GEFGK.PAED..EEQAFKRSRNTDEMVEL.ILLQSKNAGAV.GKGGKNIKA.RT
Retrocopy METEQPEETFPNTETSGEFGKHPAEDIAEEQAFKRSRNTDEMVELAILLQSKNAGAVTGKGGKNIKAFRT

Parental  DYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG
          DYN.SVSV.DSSGPERIL.ISA.I.TIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVE.LNYQHYK.
Retrocopy DYNTSVSVLDSSGPERILRISAHIKTIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVEYLNYQHYKA

Parental  SDFDCELRLLIHQSLAGG-IIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKII
          .DFDCEL.LLIHQSLAGG...G.K....K...ENTQTTI.LFQECCPH.TDRVVLIGGKP.RVVECIKII
Retrocopy RDFDCELKLLIHQSLAGG>LLGSKVLNSKN*-ENTQTTITLFQECCPHFTDRVVLIGGKPNRVVECIKII

Parental  LDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRD
          LDLI.ESPIKG.AQPYDPNFY.ETYDY.GFTM.F.D.RGRPV.F.MRGRGGFD.M.PGRGGRPMPPSRRD
Retrocopy LDLIYESPIKGHAQPYDPNFYNETYDYDGFTMVFADHRGRPVRFLMRGRGGFDKMSPGRGGRPMPPSRRD

Parental  YDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAI
          Y..MSPR.GPPP.PP..GG..GS.A.N.PLPPPPPPRGGDLM.Y.R.GRPGDRY.G.V.FSADETWDSAI
Retrocopy YVYMSPRQGPPPLPPR*GGQSGSKAQNAPLPPPPPPRGGDLMTYNRKGRPGDRYNGVVDFSADETWDSAI

Parental  DTWSPSEWQMAYEPQVEYHTDYSYAGGRGSYGDL
          DTW..SEWQMAYEPQ.....DYSYAGG.GSYGDL
Retrocopy DTWNASEWQMAYEPQGGSRYDYSYAGGHGSYGDL

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_1815 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,