RetrogeneDB ID: retro_mmus_642

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:52119314..52119869(-)
• Located in intron of: ENSMUSG00000019893

Retrocopy information

• Ensembl ID: ENSMUSG00000093563
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hmgb2
• Ensembl ID: ENSMUSG00000054717
• Aliases: Hmgb2, C80539, HMG-2, Hmg2
• Description: high mobility group box 2 [Source:MGI Symbol;Acc:MGI:96157]

Sequence

>retro_mmus_642
ATGGGCTAAAGAGACCCCAACAAGATGTGGGACAGAATGTCCTGATAAGTCTTCTTCATGCACACCTACTGGGAGGAGGA
CGACAAGAAGCACCCCAACTTTTAGGTCAACTTTGCTGAGTTCTAAAAGAAATTGCAGGAGAGATAGAAGACCATGTCTG
CAAAGGAAAAGTCAAAGTTTGAAGATCTGGCCAAGAGCAATAATGCTCGTTATGACAGGGAGATGAAGGATTACATTCCT
CCCAATGGTGTTAAGAAAGGAAAGAAAAAAAGATCCTAATGTCCCCAAAAGACTATCATTTGCTTTTCTTCTGGTTTTGT
TCTGAATATTGACCAAGGATTAAGAGTCAGTATCCAGTATTTGGAGATACTGCAAAGAAACTGGGAGGGACATGGTCTGA
ACAATCTGCCAAAGATAAATAACTGTATGAGGAGAAAGCAGCTAAACTAAAGGAGAAGTATGAAAAGGATATTGCTGCAA
ATCATGCCAAGGGCAAAGGTGAAACAAGAAAAAATGGGTCCTGGTAGGCTAACAGGCTCAAAAAAGAAAAATGAA

Alignment

ORF - retro_mmus_642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.31 %
• Parental protein coverage: 88.57 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDLAKSDKAR
          MG..DPNK....MS...FF..T..EE..KKHP...VNFAEF.KK..ER.KTMSAKEKSKFEDLAKS..AR
Retrocopy MG*RDPNKMWDRMS**VFFMHTYWEEDDKKHPNF*VNFAEF*KKLQER*KTMSAKEKSKFEDLAKSNNAR

Parental  YDREMKNYVPPKGDKKGK-KKDPNAPKRPPSA-FFLFCSENRPKIKIEHPGLSIGDTAKKLGEMWSEQSA
          YDREMK.Y.PP.G.KKGK.KKDPN.PKR...A.FF.FCSE..P.IK...P....GDTAKKLG..WSEQSA
Retrocopy YDREMKDYIPPNGVKKGK>KKDPNVPKRLSFA>FFWFCSEY*PRIKSQYP--VFGDTAKKLGGTWSEQSA

Parental  KDKQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKK-GPGRPTGSKKKNE
          KDK..YE.KAAKLKEKYEKDIAA..AKGK.E..K..GPGR.TGSKKKNE
Retrocopy KDK*LYEEKAAKLKEKYEKDIAANHAKGKGETRKN>GPGRLTGSKKKNE

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	0.00 RPM	1.89 RPM
SRP007412_cerebellum	0.00 RPM	1.95 RPM
SRP007412_heart	0.00 RPM	4.83 RPM
SRP007412_kidney	0.00 RPM	8.49 RPM
SRP007412_liver	0.00 RPM	2.51 RPM
SRP007412_testis	0.00 RPM	37.37 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_642 was not detected

EST

No EST(s) were mapped for retro_mmus_642 retrocopy.

TSS

No TSS is located nearby retro_mmus_642 retrocopy 5' end.

Lab

retro_mmus_642 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_642 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 205 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,
Dasypus novemcinctus	ENSDNOG00000019440	4 retrocopies	retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
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	ENSMUSG00000015217	1 retrocopy	retro_mmus_273,
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,
Mus musculus	ENSMUSG00000066551	129 retrocopies	retro_mmus_1025, retro_mmus_1037, retro_mmus_1047, retro_mmus_1065, retro_mmus_1094, retro_mmus_1112, retro_mmus_1113, retro_mmus_1114, retro_mmus_1115, retro_mmus_1128, retro_mmus_1135, retro_mmus_1140, retro_mmus_1178, retro_mmus_1181, retro_mmus_1209, retro_mmus_1284, retro_mmus_1302, retro_mmus_1351, retro_mmus_1407, retro_mmus_1423, retro_mmus_1508, retro_mmus_1553, retro_mmus_1554, retro_mmus_1584, retro_mmus_1672, retro_mmus_1705, retro_mmus_1706, retro_mmus_1712, retro_mmus_1716, retro_mmus_1725, retro_mmus_1775, retro_mmus_1794, retro_mmus_1800, retro_mmus_1822, retro_mmus_1845, retro_mmus_1871, retro_mmus_1989, retro_mmus_2015, retro_mmus_2077, retro_mmus_2080, retro_mmus_2096, retro_mmus_2191, retro_mmus_2194, retro_mmus_2199, retro_mmus_2209, retro_mmus_2224, retro_mmus_2229, retro_mmus_2280, retro_mmus_2300, retro_mmus_2324, retro_mmus_2404, retro_mmus_2407, retro_mmus_2409, retro_mmus_2414, retro_mmus_2420, retro_mmus_2425, retro_mmus_2467, retro_mmus_2469, retro_mmus_2524, retro_mmus_2532, retro_mmus_2627, retro_mmus_2670, retro_mmus_2682, retro_mmus_2702, retro_mmus_2719, retro_mmus_2754, retro_mmus_2789, retro_mmus_2815, retro_mmus_2823, retro_mmus_2866, retro_mmus_2877, retro_mmus_2886, retro_mmus_292, retro_mmus_2923, retro_mmus_2936, retro_mmus_2940, retro_mmus_2954, retro_mmus_2965, retro_mmus_2977, retro_mmus_303, retro_mmus_3046, retro_mmus_3056, retro_mmus_3059, retro_mmus_3067, retro_mmus_3070, retro_mmus_3075, retro_mmus_3102, retro_mmus_3106, retro_mmus_3121, retro_mmus_3169, retro_mmus_3175, retro_mmus_319, retro_mmus_3190, retro_mmus_3199, retro_mmus_3207, retro_mmus_3239, retro_mmus_3289, retro_mmus_3322, retro_mmus_3353, retro_mmus_3375, retro_mmus_3476, retro_mmus_3494, retro_mmus_3533, retro_mmus_359, retro_mmus_3612, retro_mmus_3676, retro_mmus_3692, retro_mmus_3715, retro_mmus_418, retro_mmus_515, retro_mmus_530, retro_mmus_574, retro_mmus_599, retro_mmus_618, retro_mmus_623, retro_mmus_624, retro_mmus_634, retro_mmus_704, retro_mmus_705, retro_mmus_785, retro_mmus_813, retro_mmus_839, retro_mmus_855, retro_mmus_881, retro_mmus_903, retro_mmus_906, retro_mmus_930, retro_mmus_965, retro_mmus_981,
Nomascus leucogenys	ENSNLEG00000006662	3 retrocopies	retro_nleu_113, retro_nleu_517, retro_nleu_550,
Oryctolagus cuniculus	ENSOCUG00000000074	1 retrocopy	retro_ocun_1829,
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,