RetrogeneDB ID: retro_nleu_550

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:37307369..37307943(+)
• Located in intron of: ENSNLEG00000005223

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSNLEG00000006662
• Aliases: None
• Description: None

Sequence

>retro_nleu_550
CAAGGCAATTCCAAGAAGCTAAGAGGCAGAATGTCATCACATGCGTTCTTTGTGCAGATTCGCCAGGAGAAGCACAAGAA
GCACCCAGATACTCCAGTCATCATCTCAGAGTTTTCTAAGAAGGGCTTCAGAGAAATGGAAGGCCACGTCTGCTAAAGGG
AAGGGAAAAGTTGAAGACACGGCAAAGGCAGACAAGTTTCATCATGAAAGAAATGAAAACCTACATCCCTCCTAAAGGGG
AAACAAAGAAGTTCGAGGATCCCAGTGCATCTCACAAGAGGCCTCCTTTGGCCTTTTTCTTGTTCTGTTCTTAATATTGC
CTTGAAATCAAAGGAGAAGATTCAGCCTATCCATTGGTGATGCTGCAAAGAAACTGGAAGAGACATGGAGGGACACCACT
GCAGATGACAAACAGCCTTTTGACAAGAAGGCTGCAAAGCCGAAGGAAAAATGCAAAAAGGATATTGCTGCATACCAAGC
TAAAGGAAAGCCTGATGCAGCAAAAATGAGAATGATCAAGGCTGAAAAAAGCAAGAAAAAGGAGGAGGATGAGGAAGATG
AAGAAGACGATGAA

Alignment

ORF - retro_nleu_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.33 %
• Parental protein coverage: 92.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKK-CSERWKTMSAKEKSKFEDMAKSDKARY
          .G...K.RG.MSS.AFFVQ...E.H.KKHPD..V...EFSKK..SE.WK..SAK.K.K.ED.AK.DK...
Retrocopy QGNSKKLRGRMSSHAFFVQIRQEKH-KKHPDTPVIISEFSKK>ASEKWKATSAKGKGKVEDTAKADKFHH

Parental  DREMKNYVP-PKGDKKGKKKDPNAP-KRPPSAFFLFCSEHRPKIKSEHP-GLSIGDTAKKLGEMWSEQSA
          .R...N..P.PKG..K.K..DP.A..KRPP.AFFLFCS.....IK.E....LSIGD.AKKL.E.W....A
Retrocopy ERN-ENLHP>PKGETK-KFEDPSASHKRPPLAFFLFCS*YCLEIKGEDS<SLSIGDAAKKLEETWRDTTA

Parental  KDKQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKKGPGRPTGSKKKNEPEDEEEEEE
          .DKQP...KAAK.KEK..KDIAAY.AKGK..A.K........SKKK.E.E..EE..E
Retrocopy DDKQPFDKKAAKPKEKCKKDIAAYQAKGKPDAAKMRMIKAEKSKKKEEDEEDEEDDE

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_550 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 25 parental genes, and 123 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015101	1 retrocopy	retro_btau_58,
Callithrix jacchus	ENSCJAG00000005112	2 retrocopies	retro_cjac_2555, retro_cjac_832,
Cavia porcellus	ENSCPOG00000003552	4 retrocopies	retro_cpor_1100, retro_cpor_604, retro_cpor_890, retro_cpor_980,
Dasypus novemcinctus	ENSDNOG00000019440	4 retrocopies	retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Erinaceus europaeus	ENSEEUG00000012238	8 retrocopies	retro_eeur_118, retro_eeur_223, retro_eeur_345, retro_eeur_49, retro_eeur_54, retro_eeur_661, retro_eeur_702, retro_eeur_86,
Echinops telfairi	ENSETEG00000010379	3 retrocopies	retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi	ENSETEG00000016379	1 retrocopy	retro_etel_414,
Felis catus	ENSFCAG00000004218	2 retrocopies	retro_fcat_279, retro_fcat_52,
Homo sapiens	ENSG00000164104	1 retrocopy	retro_hsap_3663,
Gorilla gorilla	ENSGGOG00000015882	1 retrocopy	retro_ggor_2474,
Loxodonta africana	ENSLAFG00000010417	3 retrocopies	retro_lafr_1096, retro_lafr_1142, retro_lafr_595,
Macropus eugenii	ENSMEUG00000002256	3 retrocopies	retro_meug_1920, retro_meug_1989, retro_meug_550,
Myotis lucifugus	ENSMLUG00000026303	4 retrocopies	retro_mluc_1113, retro_mluc_1381, retro_mluc_1726, retro_mluc_2011,
Monodelphis domestica	ENSMODG00000003527	3 retrocopies	retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Mustela putorius furo	ENSMPUG00000001919	9 retrocopies	retro_mputfur_1134, retro_mputfur_1167, retro_mputfur_1379, retro_mputfur_1475, retro_mputfur_1631, retro_mputfur_1633, retro_mputfur_1644, retro_mputfur_940, retro_mputfur_989,
Mus musculus	ENSMUSG00000054717	23 retrocopies	retro_mmus_1477, retro_mmus_1745, retro_mmus_1974, retro_mmus_1975, retro_mmus_2269, retro_mmus_2527, retro_mmus_2528, retro_mmus_2529, retro_mmus_2530, retro_mmus_2531, retro_mmus_2843, retro_mmus_2884, retro_mmus_3248, retro_mmus_3426, retro_mmus_461, retro_mmus_626, retro_mmus_642, retro_mmus_796, retro_mmus_861, retro_mmus_901, retro_mmus_902, retro_mmus_904, retro_mmus_905,
Nomascus leucogenys	ENSNLEG00000000720	33 retrocopies	retro_nleu_1148, retro_nleu_1165, retro_nleu_1241, retro_nleu_1271, retro_nleu_1393, retro_nleu_1461, retro_nleu_1633, retro_nleu_1746, retro_nleu_1932, retro_nleu_2160, retro_nleu_2210, retro_nleu_2377, retro_nleu_2512, retro_nleu_2517, retro_nleu_2637, retro_nleu_2681, retro_nleu_2708, retro_nleu_2752, retro_nleu_278, retro_nleu_2798, retro_nleu_2859, retro_nleu_292, retro_nleu_301, retro_nleu_322, retro_nleu_345, retro_nleu_393, retro_nleu_520, retro_nleu_576, retro_nleu_602, retro_nleu_875, retro_nleu_885, retro_nleu_968, retro_nleu_984,
Nomascus leucogenys	ENSNLEG00000006662	3 retrocopies	retro_nleu_113, retro_nleu_517, retro_nleu_550 ,
Oryctolagus cuniculus	ENSOCUG00000000074	1 retrocopy	retro_ocun_1829,
Otolemur garnettii	ENSOGAG00000017149	3 retrocopies	retro_ogar_3117, retro_ogar_3323, retro_ogar_3336,
Pongo abelii	ENSPPYG00000015204	3 retrocopies	retro_pabe_297, retro_pabe_3005, retro_pabe_3380,
Pan troglodytes	ENSPTRG00000016597	3 retrocopies	retro_ptro_19, retro_ptro_2484, retro_ptro_2789,
Rattus norvegicus	ENSRNOG00000013167	2 retrocopies	retro_rnor_173, retro_rnor_54,
Ictidomys tridecemlineatus	ENSSTOG00000023980	2 retrocopies	retro_itri_1720, retro_itri_880,
Tursiops truncatus	ENSTTRG00000015650	1 retrocopy	retro_ttru_1640,