RetrogeneDB ID: retro_pabe_3005

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:135699536..135700011(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSPPYG00000015204
• Aliases: None
• Description: high mobility group box 2 [Source:HGNC Symbol;Acc:5000]

Sequence

>retro_pabe_3005
CACAGCATTCTTATGCAAACTTGTCGTGAGGAGCACAAGAAGCAGCACGAAGATGCTTCGGTCAATTTCTCAGAATTTTC
TAAGACGTGCTCAGAGAGGTGGAAGGCCATGTCTGCTAAAGAGAAAGAAAAATGTGAAGATATGGCAGAGGCGGACAAGG
CCTGTTATGAAAGAGAAATGAGAACCTGTATCCCTCCTAAAGGGGAGACAAAAAAGAAGTTCAAGGATCCCAATGCACAC
AAGAGGCCTCCTTTGGCCTTTTTCTTGTTGTGTTCTAAGTATCACTAAAAAATCAAAGGAGAACATCCATCCTGGCCTAT
CCATCGGTAGTGTTGTGAAGAAGGTGGGAAAGCTGTGGAATGACACAGCTGCAGATGACAAGCATCCTTAGGAAAAGAAG
GCTGTGAACCTGAAGGAAAAATATGAAAAGGATATTGCTCCACACCAAGCTAAAGGAAAACCTGATGCAGTTAAA

Alignment

ORF - retro_pabe_3005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.38 %
• Parental protein coverage: 74.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKARYDREMKNYVPPKGDK
          .....QTCREEHKK.H.D.SVNF.EFSK.CSERWK.MSAKEK.K.EDMA..DKA.Y.REM....PPKG..
Retrocopy HSILMQTCREEHKKQHEDASVNFSEFSKTCSERWKAMSAKEKEKCEDMAEADKACYEREMRTCIPPKGET

Parental  KGKKKDPNAPKRPPSA-FFLFCSEH-RPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKE
          K.K.KDPNA.KRPP.A.F.L....H........HPGLSIG...KK.G..W....A.DK.P.E.KA..LKE
Retrocopy KKKFKDPNAHKRPPLAFFLLCSKYH>KKSKENIHPGLSIGSVVKKVGKLWNDTAADDKHP*EKKAVNLKE

Parental  KYEKDIAAYRAKGKSEAGK
          KYEKDIA...AKGK..A.K
Retrocopy KYEKDIAPHQAKGKPDAVK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.11 RPM	11.67 RPM
SRP007412_cerebellum	0.00 RPM	12.40 RPM
SRP007412_heart	0.00 RPM	15.08 RPM
SRP007412_kidney	0.00 RPM	17.40 RPM
SRP007412_liver	0.00 RPM	22.95 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3005 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3005 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3005 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3663
Pan troglodytes	retro_ptro_2484
Gorilla gorilla	retro_ggor_2474

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 147 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	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	ENSPPYG00000005546	35 retrocopies	retro_pabe_1023, retro_pabe_1125, retro_pabe_1254, retro_pabe_1334, retro_pabe_1500, retro_pabe_159, retro_pabe_1724, retro_pabe_1831, retro_pabe_1973, retro_pabe_1997, retro_pabe_2070, retro_pabe_2089, retro_pabe_2194, retro_pabe_222, retro_pabe_2313, retro_pabe_2362, retro_pabe_2406, retro_pabe_2444, retro_pabe_264, retro_pabe_2732, retro_pabe_2751, retro_pabe_2752, retro_pabe_2777, retro_pabe_2953, retro_pabe_2966, retro_pabe_3008, retro_pabe_3365, retro_pabe_3523, retro_pabe_3684, retro_pabe_3757, retro_pabe_452, retro_pabe_511, retro_pabe_522, retro_pabe_761, retro_pabe_762,
Pongo abelii	ENSPPYG00000015204	3 retrocopies	retro_pabe_297, retro_pabe_3005 , retro_pabe_3380,
Pongo abelii	ENSPPYG00000020818	22 retrocopies	retro_pabe_1207, retro_pabe_1411, retro_pabe_1505, retro_pabe_1580, retro_pabe_1823, retro_pabe_1825, retro_pabe_1927, retro_pabe_2339, retro_pabe_2538, retro_pabe_2712, retro_pabe_2816, retro_pabe_3000, retro_pabe_3041, retro_pabe_3144, retro_pabe_3387, retro_pabe_3685, retro_pabe_3813, retro_pabe_410, retro_pabe_442, retro_pabe_560, retro_pabe_632, retro_pabe_784,
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,