RetrogeneDB ID: retro_cfam_1392

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:83629468..83629753(-)
• Located in intron of: ENSCAFG00000016354

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN1
• Ensembl ID: ENSCAFG00000010045
• Aliases: None
• Description: high mobility group nucleosome binding domain 1 [Source:HGNC Symbol;Acc:4984]

Sequence

>retro_cfam_1392
GTGCCCAAGAGGAAGGTCAGCTCTGCTGAGGGGGCAGTAAAGGAGGAGCCAAGAGGAGCAAGGTTGTCATCTAAACCTGC
TTCTGCAGAAGTGGAAGCCAATCCAAAAATGGCAGCAGGAAAGGATAAATCTTCAGATAAAAAAGTGCAAATAAAAGGGA
AAATGGACACAAAGAGGAAAAAGGCTGAAGAGACTCATGAAGAAACAAGACTTACCTACAGAAAACAGAGAAACTAAAAA
TGAGGAGAGTCTGCCTGTGATGCAACAGGAGAGAAAGAAGCCAAG

Alignment

ORF - retro_cfam_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.34 %
• Parental protein coverage: 98.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKRKVSSAEGAAKEEPKRRSARLSAKPAPAKVETKPKKAAGKDKSSDKKVQTK-GKRGAKGKQAEVANQ
          .PKRKVSSAEGA.KEEP..R.ARLS.KPA.A.VE..PK.AAGKDKSSDKKVQ.K.GK....GK.......
Retrocopy VPKRKVSSAEGAVKEEP--RGARLSSKPASAEVEANPKMAAGKDKSSDKKVQIK>GKWTQRGKRLKRLMK

Parental  ETKEDLPAENGETKNEES-PASDEAGEKEAK
          ..K.DLP.EN.ETKNEES..A.D..GEKEAK
Retrocopy --KQDLPTENRETKNEES<SACDATGEKEAK

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	0.00 RPM	79.71 RPM
SRP017611_brain	0.00 RPM	21.04 RPM
SRP017611_kidney	0.00 RPM	65.31 RPM
SRP017611_liver	0.00 RPM	20.38 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1392 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1392 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 118 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018768	12 retrocopies	retro_btau_1178, retro_btau_1475, retro_btau_1560, retro_btau_1746, retro_btau_1801, retro_btau_388, retro_btau_504, retro_btau_572, retro_btau_607, retro_btau_617, retro_btau_897, retro_btau_928,
Canis familiaris	ENSCAFG00000010045	12 retrocopies	retro_cfam_1056, retro_cfam_1233, retro_cfam_1318, retro_cfam_1392 , retro_cfam_1522, retro_cfam_1667, retro_cfam_1904, retro_cfam_2202, retro_cfam_292, retro_cfam_404, retro_cfam_634, retro_cfam_649,
Cavia porcellus	ENSCPOG00000002336	7 retrocopies	retro_cpor_1129, retro_cpor_1389, retro_cpor_334, retro_cpor_349, retro_cpor_4, retro_cpor_884, retro_cpor_949,
Monodelphis domestica	ENSMODG00000020972	5 retrocopies	retro_mdom_1085, retro_mdom_109, retro_mdom_284, retro_mdom_755, retro_mdom_88,
Otolemur garnettii	ENSOGAG00000010329	35 retrocopies	retro_ogar_1062, retro_ogar_1186, retro_ogar_1245, retro_ogar_1304, retro_ogar_1355, retro_ogar_1437, retro_ogar_1527, retro_ogar_1529, retro_ogar_175, retro_ogar_1812, retro_ogar_1901, retro_ogar_1932, retro_ogar_2057, retro_ogar_2311, retro_ogar_2325, retro_ogar_2522, retro_ogar_2523, retro_ogar_266, retro_ogar_2712, retro_ogar_2729, retro_ogar_278, retro_ogar_2913, retro_ogar_2964, retro_ogar_3095, retro_ogar_3133, retro_ogar_3138, retro_ogar_3155, retro_ogar_333, retro_ogar_3354, retro_ogar_370, retro_ogar_393, retro_ogar_657, retro_ogar_699, retro_ogar_723, retro_ogar_958,
Pongo abelii	ENSPPYG00000011426	25 retrocopies	retro_pabe_1066, retro_pabe_1149, retro_pabe_1172, retro_pabe_1190, retro_pabe_123, retro_pabe_1264, retro_pabe_1302, retro_pabe_1504, retro_pabe_1604, retro_pabe_1842, retro_pabe_2152, retro_pabe_2211, retro_pabe_2284, retro_pabe_2380, retro_pabe_251, retro_pabe_2518, retro_pabe_2771, retro_pabe_3086, retro_pabe_3648, retro_pabe_3825, retro_pabe_504, retro_pabe_698, retro_pabe_699, retro_pabe_702, retro_pabe_760,
Pan troglodytes	ENSPTRG00000031426	22 retrocopies	retro_ptro_1256, retro_ptro_1299, retro_ptro_1301, retro_ptro_1454, retro_ptro_1556, retro_ptro_1740, retro_ptro_1821, retro_ptro_1830, retro_ptro_2058, retro_ptro_2290, retro_ptro_2559, retro_ptro_2716, retro_ptro_3119, retro_ptro_3278, retro_ptro_363, retro_ptro_463, retro_ptro_586, retro_ptro_61, retro_ptro_637, retro_ptro_696, retro_ptro_970, retro_ptro_980,