RetrogeneDB ID: retro_ptro_2484

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:134180642..134181154(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSPTRG00000016597
• Aliases: None
• Description: None

Sequence

>retro_ptro_2484
CACAGCATTCTTGTGCAAACTTGTCGGGAGGAGCACAAGAAGCAGCACGAAGACGCTCCGGTCAATTTCTTAGAATTTTC
TAAGACGTGCTCAGAGAGGTGGAAGACCATGTCTGCTAAAGAGAAAAGAAAAATGTGAAGATATGGCAGAGGCGAACAAG
ACCTGTTATGAAAGAGAAATGAGAACCTGTATCCCTCCTAAAGGGGAGACAAAAAAGAAGTTCAAGGATCCCAATGCACA
CAAGAGGCCTCCTTTGGCCTTTTTCTTGTTGTGTTCTAAGTATCACTAAAGAATCAAAGGAGAACATCCATCCTGGCCTA
TCCATTGGTGGTGTTGTGAAGAAGGTGGGAAAGCTGTGGAATGACACAGCTGCAGATGACAAGCATCCTTAGGAAAAGAA
GGCTGTGAACCTGAAGAAAAAATATGAAAAGGATATTGCTCCACAACAAGCTAAAGGAAAACCTGATGCAGTTAAAGAGG
GAGTTGCCAAGGCTGAGAAAGGTAAGAAAAAG

Alignment

ORF - retro_ptro_2484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.98 %
• Parental protein coverage: 80.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKF-EDMAKSDKARYDREMKNYVPPKGD
          ....VQTCREEHKK.H.D..VNF.EFSK.CSERWKTMSAKEK.K..EDMA...K..Y.REM....PPKG.
Retrocopy HSILVQTCREEHKKQHEDAPVNFLEFSKTCSERWKTMSAKEKRKM>EDMAEANKTCYEREMRTCIPPKGE

Parental  KKGKKKDPNAPKRPPSA-FFLFCSEH-RPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLK
          .K.K.KDPNA.KRPP.A.F.L....H........HPGLSIG...KK.G..W....A.DK.P.E.KA..LK
Retrocopy TKKKFKDPNAHKRPPLAFFLLCSKYH>KESKENIHPGLSIGGVVKKVGKLWNDTAADDKHP*EKKAVNLK

Parental  EKYEKDIAAYRAKGKSEAGKKGPGRPTGSKKK
          .KYEKDIA...AKGK..A.K.G.......KKK
Retrocopy KKYEKDIAPQQAKGKPDAVKEGVAKAEKGKKK

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	0.05 RPM	10.71 RPM
SRP007412_cerebellum	0.00 RPM	21.47 RPM
SRP007412_heart	0.03 RPM	26.61 RPM
SRP007412_kidney	0.00 RPM	21.42 RPM
SRP007412_liver	0.00 RPM	19.44 RPM
SRP007412_testis	0.00 RPM	305.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2484 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2484 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3663
Gorilla gorilla	retro_ggor_2474
Pongo abelii	retro_pabe_3005

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 112 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	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,
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,
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,