RetrogeneDB ID: retro_ecab_871

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:12765410..12765710(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBD2
• Ensembl ID: ENSECAG00000015810
• Aliases: None
• Description: pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2 [Source:HGNC Symbol;Acc:24474]

Sequence

>retro_ecab_871
TCAGCACATGCTCACTGGTTGGCAGCAGAGGAAAGGGACCGCGTTATCCTTGACCTTAAAGCAGTAGAATGATCGGAGTT
AAGTGAGAGGCTGTTTACAAGGGTTAGCATTCACAAATTTTAATCAGGCTTTTGACCTCATGTCCCAAGTTGCCCCACAG
GCAGAGAAAATGAATCATCACCCAGAATGGCTCAATGTGTACAACAAGGTCTAGATAACTCTCACCTCACATGACTGTGG
TGGACTCACCAAAAGAGAGTGTAAGTGGCCCAGTTTACTGAAAAAGCAGCTGCTCCTGTG

Alignment

ORF - retro_ecab_871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SADAHRLTAEERTQVILDLKAAGWSELSERDAIYKEFSFKNF-NQAFGFMSRVALQAEKMNHHPEWFNVY
          SA.AH.L.AEER..VILDLKA...SELSER.......S...F.NQAF..MS.VA.QAEKMNHHPEW.NVY
Retrocopy SAHAHWLAAEERDRVILDLKAVE*SELSER--LFTRVSIHKF>NQAFDLMSQVAPQAEKMNHHPEWLNVY

Parental  NKVQITLTSHDCGGLTKRDVK-LAKFIEKAAASV
          NKV.ITLTSHDCGGLTKR..K..A.F.EKAAA.V
Retrocopy NKV*ITLTSHDCGGLTKRECK<VAQFTEKAAAPV

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
SRP021940_articular_cartilage	0.00 RPM	1.30 RPM
SRP021940_cerebellum	0.00 RPM	2.34 RPM
SRP021940_embryo	0.00 RPM	3.73 RPM
SRP021940_placental_villous	0.00 RPM	2.84 RPM
SRP021940_synovial_membrane	0.00 RPM	3.24 RPM
SRP021940_testis	0.06 RPM	4.73 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_871 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_871 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_871 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000019125	2 retrocopies	retro_dnov_645, retro_dnov_660,
Equus caballus	ENSECAG00000015810	2 retrocopies	retro_ecab_489, retro_ecab_871 ,
Erinaceus europaeus	ENSEEUG00000007051	1 retrocopy	retro_eeur_190,
Echinops telfairi	ENSETEG00000016658	2 retrocopies	retro_etel_1252, retro_etel_75,
Macropus eugenii	ENSMEUG00000003784	1 retrocopy	retro_meug_1185,
Myotis lucifugus	ENSMLUG00000012638	1 retrocopy	retro_mluc_1445,
Monodelphis domestica	ENSMODG00000014351	1 retrocopy	retro_mdom_1369,
Pteropus vampyrus	ENSPVAG00000000384	2 retrocopies	retro_pvam_63, retro_pvam_750,
Tursiops truncatus	ENSTTRG00000016874	3 retrocopies	retro_ttru_1135, retro_ttru_359, retro_ttru_511,