RetrogeneDB ID: retro_nleu_1668

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397303.1:998877..999748(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH1
• Ensembl ID: ENSNLEG00000026658
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H1 (H) [Source:HGNC Symbol;Acc:5041]

Sequence

>retro_nleu_1668
ATGATGTCGGGCACCAAAGGTGGAGAGGGGTTTATGTTGAAGGTCCATGGCTTGCCCTGGTCTTGCTTGGCCGATGAAGT
GCAGTGTTTTTTTCTGACTGCAAAATTGAAACTAAGGCTCAAGGTATTTGTTTCATCTACACCAGAGAAGGCAGGCTGGG
TGGCAAGGCTTTTGTTGAACTTGAATCAGAAGATGAAGTCAAATTGGCCCTGAAAAAAAGACAGAGAAACTATGGGACAC
AATTTTGTTGAAGCATTCAAGTCAAACAACGTTGAAATGGATTGGGTGTTGAAGCATACTGGTCCAAATAGTCCTGACAT
GGCCAGTGATGGCTTTGTACAGCTTAGAGGACTTCCCTTTGAATGCAGCAAGGAAGAAATTGTTCAGTTCTTCTCAGGGT
TGGAAATCATGCCAAATGGGATAACATTGCCAGTGGACTCCAGGGGAGGAGTACAGGGGAGGCCTTTGTGCAGTTTGCTT
CACAGGAAATAACTGAAAAGGCTCTAAAGAAACACAAGGAAAGAATAGGGCATAGGTATATTGAAATCTTTAAGAGCAGC
AGAGCTGAAGTTAGAACTCACTACAATCCACCATAAAAGCTTATGGCTATGCAGCGGCCAGGTCCCATGACAGACCTGGT
TCTGGCAGAGGGTTTAACAGCATTGGCAGAGGAGCTGGCTTTCAGAGGATGAGGCACGGTGCTTATGGTGGAGGATATGG
AGCCTATGACAATTATAATGGCTATGGCTATGGATTTGGGTCAGACAGATTTGGAAGAGACCTCAATTATTGTTTTTCAG
GAATGTCTGATCACAAATATGGAGACGGTGGCTCTACCTTCCAGAGCACAACAGGACACTGTGTATACATG

Alignment

ORF - retro_nleu_1668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.2 %
• Parental protein coverage: 62.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MMLGTEGGEGFVVKVRGLPWSCSADEVQRFF-SDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKL
          MM.GT.GGEGF..KV.GLPWSC.ADEVQ.FF.SDCKI...AQGI.FIYTREGR..G.AFVELESEDEVKL
Retrocopy MMSGTKGGEGFMLKVHGLPWSCLADEVQCFF<SDCKIETKAQGICFIYTREGRLGGKAFVELESEDEVKL

Parental  ALKK-DRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVP
          ALKK.DRETMGH..VE.FKSNNVEMDWVLKHTGPNSPD.A.DGFV.LRGLPF.CSKEEIVQFFSGLEI.P
Retrocopy ALKK>DRETMGHNFVEAFKSNNVEMDWVLKHTGPNSPDMASDGFVQLRGLPFECSKEEIVQFFSGLEIMP

Parental  NGITLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRP
          NGITLPVD..QGRSTGEAFVQFASQEI.EKALKKHKERIGHRYIEIFKSSRAEVRTHY.PP.KLMAMQRP
Retrocopy NGITLPVD<LQGRSTGEAFVQFASQEITEKALKKHKERIGHRYIEIFKSSRAEVRTHYNPP*KLMAMQRP

Parental  GP-YDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRY
          GP..DRPG.GRG.NSIGRGAGF.RMR.GAYGGGYG.YD.YNGY..GYGFGSDRFGRDLNYCFSGMSDH.Y
Retrocopy GP<HDRPGSGRGFNSIGRGAGFQRMRHGAYGGGYGAYDNYNGY--GYGFGSDRFGRDLNYCFSGMSDHKY

Parental  GDGGSTFQSTTGHCVHM
          GDGGSTFQSTTGHCV.M
Retrocopy GDGGSTFQSTTGHCVYM

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_1668 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 22 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009389	1 retrocopy	retro_btau_130,
Canis familiaris	ENSCAFG00000000336	2 retrocopies	retro_cfam_200, retro_cfam_230,
Choloepus hoffmanni	ENSCHOG00000003841	4 retrocopies	retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus	ENSCJAG00000009931	1 retrocopy	retro_cjac_127,
Dipodomys ordii	ENSDORG00000005453	1 retrocopy	retro_dord_3,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Echinops telfairi	ENSETEG00000011303	1 retrocopy	retro_etel_50,
Gorilla gorilla	ENSGGOG00000025844	2 retrocopies	retro_ggor_1299, retro_ggor_177,
Myotis lucifugus	ENSMLUG00000016625	1 retrocopy	retro_mluc_124,
Macaca mulatta	ENSMMUG00000010843	1 retrocopy	retro_mmul_2,
Monodelphis domestica	ENSMODG00000009436	3 retrocopies	retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Mustela putorius furo	ENSMPUG00000000693	1 retrocopy	retro_mputfur_156,
Mus musculus	ENSMUSG00000007850	1 retrocopy	retro_mmus_142,
Nomascus leucogenys	ENSNLEG00000007721	1 retrocopy	retro_nleu_1973,
Nomascus leucogenys	ENSNLEG00000026658	3 retrocopies	retro_nleu_1668 , retro_nleu_28, retro_nleu_48,
Ochotona princeps	ENSOPRG00000003513	1 retrocopy	retro_opri_11,
Procavia capensis	ENSPCAG00000006715	1 retrocopy	retro_pcap_4,
Pteropus vampyrus	ENSPVAG00000007670	1 retrocopy	retro_pvam_23,
Sorex araneus	ENSSARG00000003024	1 retrocopy	retro_sara_29,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,
Ictidomys tridecemlineatus	ENSSTOG00000016376	2 retrocopies	retro_itri_66, retro_itri_78,
Vicugna pacos	ENSVPAG00000007485	2 retrocopies	retro_vpac_594, retro_vpac_614,