RetrogeneDB ID: retro_sscr_66

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:22163898..22164171(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000020696
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HMGN2
• Ensembl ID: ENSSSCG00000003555
• Aliases: HMGN2, HMG17
• Description: Sus scrofa high mobility group nucleosomal binding domain 2 (HMGN2), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001244112]

Sequence

>retro_sscr_66
ATGCCTAAGAGAAAGGCCAAAGGAGATGCTAAAGGTGACAAAGCAAAGGCGAAAGATGAGCCACAGAGAAGATCGGCACG
GTTGTCTGCTAAACCTGCCCCTCCAAAACCAGAGCCCAGGCCGAAAAAAGCCCTTGCAAAGAAGGCAGAGAAGCTGGCGA
AAGGGAGAAAGGGGAAAGCCGAAGGTGGCAAGGATGGGAACAACCCAGCCAAAAACCGAGATGCCTCCACAGACCAGTCA
CAGAAAGCAGAAAGCGCTGGGGATGCCAAGTGA

Alignment

ORF - retro_sscr_66 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKDGNNPA
          MPKRKA.GDAKGDKAK.KDEPQRRSARLSAKPAPPKPEP.PKKA.AKK.EK..KG.KGKA..GKDGNNPA
Retrocopy MPKRKAKGDAKGDKAKAKDEPQRRSARLSAKPAPPKPEPRPKKALAKKAEKLAKGRKGKAEGGKDGNNPA

Parental  ENGDAKTDQAQKAEGAGDAK
          .N.DA.TDQ.QKAE.AGDAK
Retrocopy KNRDASTDQSQKAESAGDAK

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
SRP014902_placenta	3.98 RPM	67.29 RPM
SRP014902_testis	7.78 RPM	249.37 RPM
SRP018288_heart	16.29 RPM	134.50 RPM
SRP018288_kidney	8.67 RPM	204.60 RPM
SRP018288_liver	5.44 RPM	99.94 RPM
SRP018288_lung	13.34 RPM	150.50 RPM
SRP018856_adipose	9.06 RPM	151.03 RPM
SRP035408_brain	6.57 RPM	83.09 RPM
SRP035408_liver	5.40 RPM	128.99 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_66 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_66 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_66 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_100
Pan troglodytes	retro_ptro_59
Gorilla gorilla	retro_ggor_162
Pongo abelii	retro_pabe_206
Canis familiaris	retro_cfam_38

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 138 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038104	7 retrocopies	retro_btau_1041, retro_btau_1160, retro_btau_1200, retro_btau_1292, retro_btau_1297, retro_btau_1684, retro_btau_482,
Canis familiaris	ENSCAFG00000023168	35 retrocopies	retro_cfam_1043, retro_cfam_1188, retro_cfam_1314, retro_cfam_1360, retro_cfam_1519, retro_cfam_1546, retro_cfam_1593, retro_cfam_1606, retro_cfam_1629, retro_cfam_1681, retro_cfam_1708, retro_cfam_1784, retro_cfam_1989, retro_cfam_2060, retro_cfam_2097, retro_cfam_2133, retro_cfam_266, retro_cfam_317, retro_cfam_324, retro_cfam_351, retro_cfam_353, retro_cfam_38, retro_cfam_381, retro_cfam_410, retro_cfam_446, retro_cfam_538, retro_cfam_623, retro_cfam_628, retro_cfam_705, retro_cfam_745, retro_cfam_783, retro_cfam_795, retro_cfam_821, retro_cfam_845, retro_cfam_860,
Echinops telfairi	ENSETEG00000013571	33 retrocopies	retro_etel_1035, retro_etel_1097, retro_etel_1210, retro_etel_1253, retro_etel_1282, retro_etel_1298, retro_etel_1314, retro_etel_1346, retro_etel_1398, retro_etel_1582, retro_etel_165, retro_etel_1690, retro_etel_1710, retro_etel_178, retro_etel_1836, retro_etel_1845, retro_etel_1939, retro_etel_1945, retro_etel_1951, retro_etel_1961, retro_etel_2079, retro_etel_253, retro_etel_292, retro_etel_298, retro_etel_446, retro_etel_481, retro_etel_505, retro_etel_511, retro_etel_571, retro_etel_61, retro_etel_768, retro_etel_819, retro_etel_881,
Felis catus	ENSFCAG00000012812	3 retrocopies	retro_fcat_1842, retro_fcat_4, retro_fcat_530,
Macropus eugenii	ENSMEUG00000010966	8 retrocopies	retro_meug_1178, retro_meug_126, retro_meug_1859, retro_meug_1910, retro_meug_1997, retro_meug_248, retro_meug_369, retro_meug_76,
Mus musculus	ENSMUSG00000003038	2 retrocopies	retro_mmus_202, retro_mmus_2582,
Pteropus vampyrus	ENSPVAG00000017269	5 retrocopies	retro_pvam_1046, retro_pvam_1059, retro_pvam_1065, retro_pvam_379, retro_pvam_4,
Sorex araneus	ENSSARG00000013139	3 retrocopies	retro_sara_12, retro_sara_17, retro_sara_176,
Sus scrofa	ENSSSCG00000003555	3 retrocopies	retro_sscr_573, retro_sscr_66 , retro_sscr_985,
Tupaia belangeri	ENSTBEG00000016632	33 retrocopies	retro_tbel_1351, retro_tbel_16, retro_tbel_1844, retro_tbel_21, retro_tbel_2219, retro_tbel_2498, retro_tbel_2670, retro_tbel_3050, retro_tbel_309, retro_tbel_3101, retro_tbel_3112, retro_tbel_3121, retro_tbel_3149, retro_tbel_320, retro_tbel_3413, retro_tbel_3462, retro_tbel_36, retro_tbel_389, retro_tbel_4058, retro_tbel_417, retro_tbel_4469, retro_tbel_448, retro_tbel_4615, retro_tbel_4644, retro_tbel_475, retro_tbel_50, retro_tbel_538, retro_tbel_62, retro_tbel_65, retro_tbel_66, retro_tbel_704, retro_tbel_732, retro_tbel_757,
Tursiops truncatus	ENSTTRG00000005681	5 retrocopies	retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,
Vicugna pacos	ENSVPAG00000008076	1 retrocopy	retro_vpac_183,