RetrogeneDB ID: retro_ptro_1115

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:56686482..56687034(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB3
• Ensembl ID: ENSPTRG00000022371
• Aliases: None
• Description: high mobility group box 3 [Source:HGNC Symbol;Acc:5004]

Sequence

>retro_ptro_1115
ATGGCTAAAGATGACCCCCAAGAAACCAAAAGGTGAGATGTCTGCTTATGCCTTCTTTATGCAGACATGCAGAGAAGAAT
GCAAGAAGAAAAACCCAGAGGTGCTTGTCAATTTCACAGAAATTTCCAAGAAGTGCTCTGAGAGGTGGAAGACAATGTGT
GGAAAAGAGAAGTCTAAGCCTGACGAAATGACCGAGGTGGATGAAGTACTCTATGATTGGGGAATAAAGAATTACGGACC
AGCTAAGGGAGGCAAGAAGAAGGACCCTAAAGCCCCCAAAAGGCTACCACCTGGATTCTTCCTGTTCTGTTCAGAATTCT
GCCCCAAGGACAAATCCACAAACCCTGGCATCTCTATTGGAGATGTGGCAAAAAGGCTGAGTGAGATATGGAATAACTTG
AGTGACAGTGCATAGCTGCCTGACATCACTACGGCAGCAAGCTGAAGAAGTGTGAGAAGGGTGTTGCTGACTCTAAGTCT
AAAGGAAAGTTCGATGGTGCAAAAGTTAAAGTTGCCTGGAAAAAGGTAGACGAGGAAGAGGAGGAGGAGGAA

Alignment

ORF - retro_ptro_1115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.32 %
• Parental protein coverage: 94. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKGDP-KKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKV
          MAK.DP.KKPKG.MSAYAFF.QTCREE.KKKNPEV.VNF.E.SKKCSERWKTM.GKEKSK.DEM...D.V
Retrocopy MAKDDP>KKPKGEMSAYAFFMQTCREECKKKNPEVLVNFTEISKKCSERWKTMCGKEKSKPDEMTEVDEV

Parental  RYDREMKDYGPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEK
          .YD...K.YGPAKGG.KKKDP.APKR.P.GFFLFCSEF.PK.KSTNPGISIGDVAK.L.E.WNNL.DS..
Retrocopy LYDWGIKNYGPAKGG-KKKDPKAPKRLPPGFFLFCSEFCPKDKSTNPGISIGDVAKRLSEIWNNLSDSA*

Parental  QPYITKAA-KLKEKYEKDVADYKSKGKFDGAKGPAKVARKKVEEEDEEEE
          .P.IT.AA.KLK.K.EK.VAD.KSKGKFDGAK...KVA.KKV.EE.EEEE
Retrocopy LPDITTAA<KLK-KCEKGVADSKSKGKFDGAK--VKVAWKKVDEEEEEEE

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	0.02 RPM	15.23 RPM
SRP007412_cerebellum	0.00 RPM	12.19 RPM
SRP007412_heart	0.00 RPM	12.94 RPM
SRP007412_kidney	0.10 RPM	11.40 RPM
SRP007412_liver	0.03 RPM	34.86 RPM
SRP007412_testis	0.00 RPM	51.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1115 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1115 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 195 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005150	2 retrocopies	retro_btau_190, retro_btau_38,
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,
Echinops telfairi	ENSETEG00000015689	4 retrocopies	retro_etel_104, retro_etel_1272, retro_etel_385, retro_etel_465,
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,
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,
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,
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,
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,