RetrogeneDB ID: retro_cfam_272

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:87485561..87486630(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000028932
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSCAFG00000013497
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_cfam_272
GAGGGCCATGATCCAAAGGAACCTGAGCAGTTGAGAAAACTGTTTATTGGTGGTTTGAGCCTTGAAACTACGGATGATAG
TTTAAGAGAACATTTTGAAAAATGGGGCACACTTACAGATTGTGTGGTAATGAGAGACCCCCAAACAAAACGTTCCAGGG
GTTTTGGTTTTGTGACTTACTCTTGTGTTGAAGAGGTGGATGCAGCAATGTCAATGTGTGCCCGACCACACAAGGTTGAT
GGGCGTGTAGTGGAACCAAAGAGAGCTGCTTCTAGAGAGGATTCTGTAAAGCCTGGTGCCCATCTAACAATGAAGAAAAT
TTTTGTTGGTGGTATTAAAGAAGGTACAGAAGAATATAATTTGAGAGACTACTTTGAAAAGTATGGCAAAATTGAAACCA
TAGAAGTTATGGAAGACCGGCAGAGTGGAAAAAAAGAGGATTTGCTTTTGTAACTTTTGATGATCATGATACAGTTGATA
AAATTGTTGTTCAGAAATACCACACTATTAATGGGCATAATTGTGAAGTGAAAAAGGCCCTTTCTAAACAAGAGGTGCAG
TCTGCTGGATCGCAAAGAGTCGTGAAGGTGGATTTGGCAACTTCATGGGTCGTGGAGGAAACTTTGGAGGTGGTGGTAAT
TTTGGCTGTGGTGGAAACTTTGGTGGAAGAGGAGGCTATGGTGGTGGAGGTGGTGGCAGCAGAGGTAGTTATGGAGGAGG
TGATGGTGGATATAATGGATTTGGAGGTGATGGTGGCAACTATGGTGGTGGTCCTGGTTATAGTAGTAGAGGAGGCTATG
GTGGTGGTGGACCAGGATATGGAAACCAAGGAGGTGGATATGGTGGTGGTGGTGGAGGATACGATGGTTACAATGAAGGA
GGAAATTTTGGAGGTGGTAACTATGGTGGTGGTGGGAACTATAATGATTTTGGAAATTATAGTGGACAACAGCAATCAAA
TTATGGACCCATGAAAGGGGGCAGTTTTGGTGGAAGAAGCTCAGGCAGTCCCTATGGTGGTGGTTATGGATCTGGTGGTG
GAAGTGGTGGATATGGTAGCAGAAGGTTC

Alignment

ORF - retro_cfam_272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.64 %
• Parental protein coverage: 93.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM
          EGHDPKEPEQLRKLFIGGLS.ETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM
Retrocopy EGHDPKEPEQLRKLFIGGLSLETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM

Parental  --CARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDR
          ..CARPHKVDGRVVEPKRA.SREDSVKPGAHLT.KKIFVGGIKE.TEEYNLRDYFEKYGKIETIEVMEDR
Retrocopy SMCARPHKVDGRVVEPKRAASREDSVKPGAHLTMKKIFVGGIKEGTEEYNLRDYFEKYGKIETIEVMEDR

Parental  QSGKK-RGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQR-GRGGGSGNFMGRGGN
          QSGKK.RGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQE.QSAGSQR..R.GG.GNFMG....
Retrocopy QSGKK<RGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEVQSAGSQR<SREGGFGNFMGXXXX

Parental  FGGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQG
          ..............GRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQG
Retrocopy XXXXXXXXXXXXXXGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQG

Parental  GGYGGGGGGYDGYNEGGNFGGGNYGGGGNYNDFGNYSGQQQSNYGPMKGGSFGGRSSGSPYGGGYGSGGG
          GGYGGGGGGYDGYNEGGNFGGGNYGGGGNYNDFGNYSGQQQSNYGPMKGGSFGGRSSGSPYGGGYGSGGG
Retrocopy GGYGGGGGGYDGYNEGGNFGGGNYGGGGNYNDFGNYSGQQQSNYGPMKGGSFGGRSSGSPYGGGYGSGGG

Parental  SGGYGSRRF
          SGGYGSRRF
Retrocopy SGGYGSRRF

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	0.46 RPM	173.46 RPM
SRP017611_brain	0.24 RPM	60.97 RPM
SRP017611_kidney	0.40 RPM	51.77 RPM
SRP017611_liver	0.36 RPM	49.16 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_272 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_272 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_272 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000241	2 retrocopies	retro_cfam_408, retro_cfam_412,
Canis familiaris	ENSCAFG00000006580	16 retrocopies	retro_cfam_1080, retro_cfam_1081, retro_cfam_1170, retro_cfam_1323, retro_cfam_1616, retro_cfam_1844, retro_cfam_2017, retro_cfam_2128, retro_cfam_360, retro_cfam_564, retro_cfam_702, retro_cfam_803, retro_cfam_839, retro_cfam_855, retro_cfam_892, retro_cfam_937,
Canis familiaris	ENSCAFG00000008940	1 retrocopy	retro_cfam_1086,
Canis familiaris	ENSCAFG00000013497	12 retrocopies	retro_cfam_1214, retro_cfam_1326, retro_cfam_1388, retro_cfam_1548, retro_cfam_1690, retro_cfam_1816, retro_cfam_265, retro_cfam_272 , retro_cfam_400, retro_cfam_625, retro_cfam_65, retro_cfam_836,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pteropus vampyrus	ENSPVAG00000010380	2 retrocopies	retro_pvam_1077, retro_pvam_326,
Sus scrofa	ENSSSCG00000015988	6 retrocopies	retro_sscr_1110, retro_sscr_1152, retro_sscr_391, retro_sscr_621, retro_sscr_764, retro_sscr_927,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,