RetrogeneDB ID: retro_cfam_412

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:10618532..10618992(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPAB
• Ensembl ID: ENSCAFG00000000241
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A/B [Source:HGNC Symbol;Acc:5034]

Sequence

>retro_cfam_412
AAGAATGTTCTTGGAGGCGTGCGCTGGGATACCGGCCAAGAGGACCTAAAGGATCATTTTACCAAATTTGGGGAGGTCGT
TGACTGTCCCATAAAATCGGACCCACACAGTGGCCGGCCAAGAGGGGTTGGGTTTATCGTCTTCAAAGATGCGGCCAGTG
TGGAGAAGGTCCTAGAGCAGAAGGAACACAGGCTGCCTGGCCGCGTCGCTGACCCCAAGAAGGCCATGGCCATGGAAAAG
GACCCGGTAAAGAAAATCGTTTGTAGGGGGTCTGAATCCCGGAGCCACTGAGGAGAAGGTCAGAGAATACTTCGGCGAGT
TTGGGGAGATCGAGGCCATTGAGCTTCCAAAGGATCCAAAGTCGAATAAAAGACGAGGTTTTGTCTCCGTCACCTTTAAA
GAAGAAGGACCTGTGAAGAAGGTTCTGGAGAAAAGGTCCCGTACCATCAGCGGAAGCAAG

Alignment

ORF - retro_cfam_412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.52 %
• Parental protein coverage: 57.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVI
          K...GG..WDT...DLKD.FTKFGEVVDC.IK.DP..GR.RG.GFI.FKDAASVEKVL.QKEHRL.GRV.
Retrocopy KNVLGGVRWDTGQEDLKDHFTKFGEVVDCPIKSDPHSGRPRGVGFIVFKDAASVEKVLEQKEHRLPGRVA

Parental  DPKKAMAMKKDPVKKI-FVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKSNKRRGFVFITFKEEEPVK
          DPKKAMAM.KDPVKKI.FVGGLNP.ATEEK.REYFGEFGEIEAIELP.DPKSNKRRGFV..TFKEE.PVK
Retrocopy DPKKAMAMEKDPVKKI>FVGGLNPGATEEKVREYFGEFGEIEAIELPKDPKSNKRRGFVSVTFKEEGPVK

Parental  KVLEKKFHTISGSK
          KVLEK...TISGSK
Retrocopy KVLEKRSRTISGSK

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	28.60 RPM
SRP017611_brain	0.00 RPM	7.15 RPM
SRP017611_kidney	0.00 RPM	11.82 RPM
SRP017611_liver	0.00 RPM	8.63 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_412 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_412 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 45 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,
Homo sapiens	ENSG00000197451	1 retrocopy	retro_hsap_962,
Loxodonta africana	ENSLAFG00000001189	1 retrocopy	retro_lafr_405,
Macropus eugenii	ENSMEUG00000007909	2 retrocopies	retro_meug_169, retro_meug_246,
Myotis lucifugus	ENSMLUG00000003380	2 retrocopies	retro_mluc_2024, retro_mluc_2138,
Nomascus leucogenys	ENSNLEG00000015775	1 retrocopy	retro_nleu_1611,
Oryctolagus cuniculus	ENSOCUG00000026424	3 retrocopies	retro_ocun_1800, retro_ocun_1811, retro_ocun_950,
Otolemur garnettii	ENSOGAG00000030251	2 retrocopies	retro_ogar_3509, retro_ogar_385,
Pongo abelii	ENSPPYG00000016107	1 retrocopy	retro_pabe_821,
Pan troglodytes	ENSPTRG00000017601	1 retrocopy	retro_ptro_666,