RetrogeneDB ID: retro_mmul_1003

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:104676251..104676771(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB3
• Ensembl ID: ENSMMUG00000004633
• Aliases: None
• Description: high mobility group box 3 [Source:HGNC Symbol;Acc:5004]

Sequence

>retro_mmul_1003
ATGGCTAAATGTGATCCCAAGAAAGCAAAGGGCAAGATGTCTGTTTATGCCTTCTTTCTGCAGACGTGCAGAGAAGAACA
TAAGAAGAAAAACCCTGTCAATTTTGCAGCATTTTCCAAGAAGTGGTCTTAGAGGTAGAAGACAATGTCCGGACAAGATA
AATCTAAATTTGCTGAAACGGCAGAGGCGGATAAAGTGCACTGTGATTGGGAAATGAAGGATTATTGACCAGCTAAGGGA
GACAAGAGAAGAAGAATCCTAATGCCTTCCAAAGGCCACAGTCTGGATTCTTCCTTTTCTGCCCGGAATTCCACCCCAAG
ATCAAATCCACAAACCCTAGCATCTCTATTGGAGACGTGGCAAGAAAGCTAGTGAGATGTGGAATAACGTAAGTGACAGT
GAAAAGCAACCTTACATCACTAAGGCGGCAAAGCTGAAAGAGAATTAGGAGAAGGATGTTGCTGACTACAAGTTGAAAGG
AAAGTTTGATGGAGCAAAGGATCCTGCTAAAGTTGCCCAG

Alignment

ORF - retro_mmul_1003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.65 %
• Parental protein coverage: 88.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVR
          MAK.DPKK.KGKMS.YAFF.QTCREEHKKKN...PVNFA.FSKK.S.R.KTMSG..KSKF.E.A.ADKV.
Retrocopy MAKCDPKKAKGKMSVYAFFLQTCREEHKKKN---PVNFAAFSKKWS*R*KTMSGQDKSKFAETAEADKVH

Parental  YDREMKDYGPAKGGKK-KKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKL-GEMWNNLNDSE
          .D.EMKDY.PAKG.K..KK.PNA..RP.SGFFLFC.EF.PKIKSTNP.ISIGDVA.KL..EMWNN..DSE
Retrocopy CDWEMKDY*PAKGDKR<KKNPNAFQRPQSGFFLFCPEFHPKIKSTNPSISIGDVARKL<SEMWNNVSDSE

Parental  KQPYITKAAKLKEKYEKDVADYKSKGKFDGAKGPAKVAR
          KQPYITKAAKLKE..EKDVADYK.KGKFDGAK.PAKVA.
Retrocopy KQPYITKAAKLKEN*EKDVADYKLKGKFDGAKDPAKVAQ

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	0.11 RPM	8.85 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	5.47 RPM
SRP007412_cerebellum	0.06 RPM	3.29 RPM
SRP007412_heart	0.00 RPM	10.07 RPM
SRP007412_kidney	0.12 RPM	10.45 RPM
SRP007412_liver	0.00 RPM	3.21 RPM
SRP007412_testis	0.00 RPM	33.70 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1003 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1003 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2135
Pan troglodytes	retro_ptro_1561
Gorilla gorilla	retro_ggor_1651
Pongo abelii	retro_pabe_1927

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Parental genes homology:

Parental genes homology involve 31 parental genes, and 203 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005150	2 retrocopies	retro_btau_190, retro_btau_38,
Canis familiaris	ENSCAFG00000028715	1 retrocopy	retro_cfam_1537,
Choloepus hoffmanni	ENSCHOG00000005005	2 retrocopies	retro_chof_1891, retro_chof_2010,
Callithrix jacchus	ENSCJAG00000003936	9 retrocopies	retro_cjac_1596, retro_cjac_1950, retro_cjac_2343, retro_cjac_2469, retro_cjac_2470, retro_cjac_2738, retro_cjac_2900, retro_cjac_688, retro_cjac_965,
Dipodomys ordii	ENSDORG00000010826	4 retrocopies	retro_dord_214, retro_dord_337, retro_dord_454, retro_dord_609,
Equus caballus	ENSECAG00000020596	1 retrocopy	retro_ecab_890,
Echinops telfairi	ENSETEG00000015689	4 retrocopies	retro_etel_104, retro_etel_1272, retro_etel_385, retro_etel_465,
Felis catus	ENSFCAG00000024624	4 retrocopies	retro_fcat_1480, retro_fcat_1504, retro_fcat_265, retro_fcat_865,
Homo sapiens	ENSG00000029993	8 retrocopies	retro_hsap_1461, retro_hsap_1873, retro_hsap_2621, retro_hsap_3064, retro_hsap_3683, retro_hsap_4251, retro_hsap_4904, retro_hsap_627,
Gorilla gorilla	ENSGGOG00000027164	16 retrocopies	retro_ggor_1371, retro_ggor_1538, retro_ggor_1540, retro_ggor_1651, retro_ggor_1834, retro_ggor_2104, retro_ggor_2250, retro_ggor_2469, retro_ggor_2490, retro_ggor_2580, retro_ggor_272, retro_ggor_2944, retro_ggor_301, retro_ggor_414, retro_ggor_549, retro_ggor_618,
Loxodonta africana	ENSLAFG00000025877	1 retrocopy	retro_lafr_893,
Myotis lucifugus	ENSMLUG00000010926	4 retrocopies	retro_mluc_1055, retro_mluc_1989, retro_mluc_215, retro_mluc_529,
Macaca mulatta	ENSMMUG00000004633	20 retrocopies	retro_mmul_1003 , retro_mmul_1115, retro_mmul_1143, retro_mmul_1303, retro_mmul_1341, retro_mmul_1482, retro_mmul_1568, retro_mmul_1624, retro_mmul_1799, retro_mmul_1957, retro_mmul_2106, retro_mmul_2425, retro_mmul_2451, retro_mmul_2469, retro_mmul_2484, retro_mmul_2526, retro_mmul_267, retro_mmul_399, retro_mmul_514, retro_mmul_597,
Macaca mulatta	ENSMMUG00000023399	3 retrocopies	retro_mmul_2079, retro_mmul_320, retro_mmul_385,
Monodelphis domestica	ENSMODG00000005735	7 retrocopies	retro_mdom_1257, retro_mdom_1508, retro_mdom_1883, retro_mdom_1952, retro_mdom_587, retro_mdom_698, retro_mdom_831,
Mustela putorius furo	ENSMPUG00000011606	2 retrocopies	retro_mputfur_138, retro_mputfur_26,
Mus musculus	ENSMUSG00000015217	1 retrocopy	retro_mmus_273,
Oryctolagus cuniculus	ENSOCUG00000005986	7 retrocopies	retro_ocun_1033, retro_ocun_1913, retro_ocun_1914, retro_ocun_534, retro_ocun_568, retro_ocun_891, retro_ocun_931,
Otolemur garnettii	ENSOGAG00000001773	19 retrocopies	retro_ogar_1318, retro_ogar_1647, retro_ogar_1728, retro_ogar_187, retro_ogar_1930, retro_ogar_204, retro_ogar_2076, retro_ogar_2530, retro_ogar_2591, retro_ogar_2678, retro_ogar_2743, retro_ogar_2983, retro_ogar_3127, retro_ogar_3371, retro_ogar_343, retro_ogar_3433, retro_ogar_3479, retro_ogar_3513, retro_ogar_65,
Procavia capensis	ENSPCAG00000001945	1 retrocopy	retro_pcap_328,
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	ENSPTRG00000022371	22 retrocopies	retro_ptro_1115, retro_ptro_1211, retro_ptro_1276, retro_ptro_1429, retro_ptro_1432, retro_ptro_1561, retro_ptro_174, retro_ptro_1766, retro_ptro_2066, retro_ptro_213, retro_ptro_2218, retro_ptro_2296, retro_ptro_2477, retro_ptro_2497, retro_ptro_2608, retro_ptro_2891, retro_ptro_2944, retro_ptro_3154, retro_ptro_3271, retro_ptro_456, retro_ptro_522, retro_ptro_629,
Pteropus vampyrus	ENSPVAG00000000219	1 retrocopy	retro_pvam_356,
Rattus norvegicus	ENSRNOG00000011096	4 retrocopies	retro_rnor_1049, retro_rnor_2303, retro_rnor_2359, retro_rnor_2363,
Rattus norvegicus	ENSRNOG00000050910	5 retrocopies	retro_rnor_1956, retro_rnor_2516, retro_rnor_2625, retro_rnor_720, retro_rnor_954,
Sarcophilus harrisii	ENSSHAG00000002916	2 retrocopies	retro_shar_139, retro_shar_316,
Sus scrofa	ENSSSCG00000012745	3 retrocopies	retro_sscr_1094, retro_sscr_466, retro_sscr_467,
Ictidomys tridecemlineatus	ENSSTOG00000023908	6 retrocopies	retro_itri_1366, retro_itri_1527, retro_itri_1655, retro_itri_1749, retro_itri_777, retro_itri_909,
Tupaia belangeri	ENSTBEG00000003068	18 retrocopies	retro_tbel_1002, retro_tbel_1230, retro_tbel_1579, retro_tbel_1700, retro_tbel_1819, retro_tbel_2543, retro_tbel_2730, retro_tbel_3261, retro_tbel_3476, retro_tbel_3623, retro_tbel_3781, retro_tbel_408, retro_tbel_410, retro_tbel_4203, retro_tbel_4209, retro_tbel_4299, retro_tbel_605, retro_tbel_698,
Tursiops truncatus	ENSTTRG00000000205	2 retrocopies	retro_ttru_1187, retro_ttru_372,
Vicugna pacos	ENSVPAG00000000096	2 retrocopies	retro_vpac_245, retro_vpac_434,