RetrogeneDB ID: retro_ecab_525

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:101381817..101382114(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF10
• Ensembl ID: ENSECAG00000007794
• Aliases: None
• Description: TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa [Source:HGNC Symbol;Acc:11543]

Sequence

>retro_ecab_525
CAGTTGGAGGACTGCACACCTACAATCCCAGATAGAGTGACTGGCTACTCCCTGAACCATGCTGGCTTTGGAGCCTCAGA
TCCAGACATAACTCAGTTCATCCCCCTAACTGCTCAGAAATTCATCTCAGATATCGCCAACAATGTTGATGTCCTGTGGC
ACTGCAAAAGGAAGGGCACAGCTTCTAGCAGCTCCTGAAGCAAGAAAAGGGACCACAGGTACACTCTAAGCATAGAGGAC
TTGACTTCTACCCTTAGCAAGTATGACATCAGTATAAACAAACCACAACACTTCACC

Alignment

ORF - retro_ecab_525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 98.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIAN--DALQHCKMKGTASGSSRSKSK
          QLED.TPTIPD.VTGY.LN.AGF.ASDP.I...I.L.AQKFISDIAN..D.L.HCK.KGTAS.SS.SK..
Retrocopy QLEDCTPTIPDRVTGYSLNHAGFGASDPDITQFIPLTAQKFISDIANNVDVLWHCKRKGTASSSS*SKKR

Parental  DRKYTLTMEDLTPALSEYGINVKKPHYFT
          D..YTL..EDLT..LS.Y.I...KP..FT
Retrocopy DHRYTLSIEDLTSTLSKYDISINKPQHFT

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	19.48 RPM
SRP021940_cerebellum	0.00 RPM	26.33 RPM
SRP021940_embryo	0.00 RPM	28.08 RPM
SRP021940_placental_villous	0.00 RPM	25.16 RPM
SRP021940_synovial_membrane	0.00 RPM	27.01 RPM
SRP021940_testis	0.00 RPM	69.38 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_525 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_525 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_525 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016278	2 retrocopies	retro_amel_1088, retro_amel_297,
Canis familiaris	ENSCAFG00000006498	2 retrocopies	retro_cfam_1041, retro_cfam_992,
Dasypus novemcinctus	ENSDNOG00000000814	1 retrocopy	retro_dnov_592,
Equus caballus	ENSECAG00000007794	1 retrocopy	retro_ecab_525 ,
Erinaceus europaeus	ENSEEUG00000008412	3 retrocopies	retro_eeur_542, retro_eeur_692, retro_eeur_709,
Echinops telfairi	ENSETEG00000008886	1 retrocopy	retro_etel_2090,
Felis catus	ENSFCAG00000015390	1 retrocopy	retro_fcat_1458,
Loxodonta africana	ENSLAFG00000029330	1 retrocopy	retro_lafr_750,
Macropus eugenii	ENSMEUG00000008216	2 retrocopies	retro_meug_1645, retro_meug_992,
Myotis lucifugus	ENSMLUG00000024459	1 retrocopy	retro_mluc_1960,
Macaca mulatta	ENSMMUG00000007743	1 retrocopy	retro_mmul_1144,
Mus musculus	ENSMUSG00000043866	1 retrocopy	retro_mmus_35,
Tursiops truncatus	ENSTTRG00000004894	1 retrocopy	retro_ttru_1113,