RetrogeneDB ID: retro_cjac_2555

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:109993448..109993975(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007981
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSCJAG00000005112
• Aliases: None
• Description: high mobility group box 2 [Source:HGNC Symbol;Acc:5000]

Sequence

>retro_cjac_2555
ATGGGTAAAGGAGACCCCAACAAGCCGAGGGGCAAAATGTCCTCATACGCCTTCTTCGTGCATACCTGCTGGGAAGAGCA
CAATCAAAACACCCGGACTCTTCCGTCAATTTTGCAGAATTCTCCAAGAAGTGTTGGGAGAGATGGAAGACCATGTCTGC
AAAGGAGAAGTCGAAGTTTGAAGATATGGCGAAAAGTGACAAAGCTCGCTATGATAGGGAGATGAAAAATTACGTCTCTC
CCAAAGGTGATAAGAAAGGAAAGAAAAAGGATCCCAATGCTCCTAAAAGGCCACCATCTGCCTTCTTCCTGTTTTGCTCT
GAACATTGCCCAAAGATCAAAAGTGAACATCCAGGCCTATCCACTGGGGATACTGCAAAGAAATTGGGTGAAATATGGTC
TGAGCAGTCAGCCAAAGATAAACAACCATATGAACAGAAAGCAGCTAAGCTAAAGGAGAATTCTGAAAAGGATATTGCTG
CATATCGTGCCAAGGGCAAAAGTGAAGCAGGAAAGAAAGGCCCTGGC

Alignment

ORF - retro_cjac_2555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 85.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKGDPNKPRGKMSSYAFFVQTCREEHKK-KHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKA
          MGKGDPNKPRGKMSSYAFFV.TC.EEH...KHPDSSVNFAEFSKKC.ERWKTMSAKEKSKFEDMAKSDKA
Retrocopy MGKGDPNKPRGKMSSYAFFVHTCWEEHNQ<KHPDSSVNFAEFSKKCWERWKTMSAKEKSKFEDMAKSDKA

Parental  RYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAK
          RYDREMKNYV.PKGDKKGKKKDPNAPKRPPSAFFLFCSEH.PKIKSEHPGLS.GDTAKKLGE.WSEQSAK
Retrocopy RYDREMKNYVSPKGDKKGKKKDPNAPKRPPSAFFLFCSEHCPKIKSEHPGLSTGDTAKKLGEIWSEQSAK

Parental  DKQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKKGPG
          DKQPYEQKAAKLKE..EKDIAAYRAKGKSEAGKKGPG
Retrocopy DKQPYEQKAAKLKENSEKDIAAYRAKGKSEAGKKGPG

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
SRP051959_colon	0.33 RPM	31.77 RPM
SRP051959_heart	0.32 RPM	19.50 RPM
SRP051959_kidney	0.33 RPM	11.14 RPM
SRP051959_liver	0.17 RPM	11.16 RPM
SRP051959_lung	0.52 RPM	35.40 RPM
SRP051959_lymph_node	0.53 RPM	54.75 RPM
SRP051959_skeletal_muscle	0.17 RPM	14.92 RPM
SRP051959_spleen	0.53 RPM	49.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2555 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2555 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015101	1 retrocopy	retro_btau_58,
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,
Callithrix jacchus	ENSCJAG00000005112	2 retrocopies	retro_cjac_2555 , retro_cjac_832,
Callithrix jacchus	ENSCJAG00000021615	11 retrocopies	retro_cjac_1042, retro_cjac_1546, retro_cjac_1819, retro_cjac_1842, retro_cjac_1934, retro_cjac_2269, retro_cjac_2901, retro_cjac_2934, retro_cjac_3090, retro_cjac_718, retro_cjac_895,
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	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,
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,