RetrogeneDB ID: retro_cfam_538

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:3820865..3821134(+)
• Located in intron of: ENSCAFG00000000602

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN2
• Ensembl ID: ENSCAFG00000023168
• Aliases: HMGN2, HMG-17
• Description: Canis lupus familiaris non-histone chromosomal protein HMG-17 (HMGN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001003101]

Sequence

>retro_cfam_538
ATGCCCAAGAGAAAGGCTGAAGGGGATGCTAAAGGAGATAAAGCCAAGGTGAAGGATGAGCCGCAGAGAAGATCTGCAAG
GTTATCTGCTAAACTTGCTCCTCCAAAGCCAGAGCCCAAGCCTAAAAAGGCCCCTGTAAAGAAGGGAGAGAAAGTACCCA
AAGCTAAAAGGGGAAGGCTGATTCTGGCAAGGATGGAAATAACCCTGCAGAAAATGGAGATGCCAAAACAGATCAGGCAC
AGAAAGCTGAAGGTGCTGGAGATGCCAAG

Alignment

ORF - retro_cfam_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGK-KGKADAGKDGNNP
          MPKRKAEGDAKGDKAKVKDEPQRRSARLSAK.APPKPEPKPKKAP.KKGEKVPK.K.KGKAD.GKDGNNP
Retrocopy MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKLAPPKPEPKPKKAPVKKGEKVPKAK<KGKADSGKDGNNP

Parental  AENGDAKTDQAQKAEGAGDAK
          AENGDAKTDQAQKAEGAGDAK
Retrocopy AENGDAKTDQAQKAEGAGDAK

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
SRP012049_cerebellum	0.08 RPM	112.05 RPM
SRP017611_brain	0.08 RPM	22.87 RPM
SRP017611_kidney	0.00 RPM	60.82 RPM
SRP017611_liver	0.00 RPM	19.14 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_538 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_538 has 0 orthologous retrocopies within eutheria group .

---

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,