RetrogeneDB ID: retro_ecab_610

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:55576965..55577305(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZBTB8OS
• Ensembl ID: ENSECAG00000020982
• Aliases: None
• Description: zinc finger and BTB domain containing 8 opposite strand [Source:HGNC Symbol;Acc:24094]

Sequence

>retro_ecab_610
TTGAGAGGCTACAGCTTGACCAAGAAGCAGGAGGTAACCAAAGCCAACTTTCCTCTATCTAGTCAGAAGTATGAATACCT
GGATCACACAGCCAATGTCCAGTTACACATATGGAGAGATACTTTGCAGAGAGTCTTTAAGCACCGTATGATGGCCGTGG
TTGCTTACTTGACAGATACTAGGGTCATCAAGCCCCTGAAAATAGGAGTAAATATGCAAGGAGATGCCTTGGCAATCTTT
CTGGCTTCATGTTTTGGATAAGCAGCTTTATAAATTTAGGCCTGTTGAGTTTTTCATGCCCTGGGTAGCAAAAATATTCA
CTATTGACCAAAGGAATTTC

Alignment

ORF - retro_ecab_610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.3 %
• Parental protein coverage: 68.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRDYNLTEEQKAIKAKYPPVNRKYEYLDHTADVQLHAWGDTLEEAFEQCAMAMFGYMTDTGTVEPLQTVE
          .R.Y.LT..Q...KA..P....KYEYLDHTA.VQLH.W.DTL...F....MA...Y.TDT....PL....
Retrocopy LRGYSLTKKQEVTKANFPLSSQKYEYLDHTANVQLHIWRDTLQRVFKHRMMAVVAYLTDTRVIKPLK-IG

Parental  VETQGDDL-ESLLFHFLDEWLYKFSADEFFIPREAKVLNIDQRNF
          V..QGD.L..S...H.LD..LYKF...EFF.P..AK...IDQRNF
Retrocopy VNMQGDAL>QSFWLHVLDKQLYKFRPVEFFMPWVAKIFTIDQRNF

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	0.83 RPM	3.54 RPM
SRP021940_cerebellum	0.00 RPM	3.74 RPM
SRP021940_embryo	1.66 RPM	11.48 RPM
SRP021940_placental_villous	0.34 RPM	6.83 RPM
SRP021940_synovial_membrane	0.30 RPM	5.98 RPM
SRP021940_testis	0.26 RPM	3.64 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_610 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_610 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_610 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010550	1 retrocopy	retro_cfam_2152,
Choloepus hoffmanni	ENSCHOG00000004061	2 retrocopies	retro_chof_1005, retro_chof_1158,
Cavia porcellus	ENSCPOG00000015349	2 retrocopies	retro_cpor_356, retro_cpor_903,
Dasypus novemcinctus	ENSDNOG00000001861	2 retrocopies	retro_dnov_1056, retro_dnov_2193,
Equus caballus	ENSECAG00000020982	1 retrocopy	retro_ecab_610 ,
Felis catus	ENSFCAG00000000700	1 retrocopy	retro_fcat_703,
Homo sapiens	ENSG00000176261	2 retrocopies	retro_hsap_2396, retro_hsap_2992,
Gorilla gorilla	ENSGGOG00000007519	2 retrocopies	retro_ggor_2072, retro_ggor_231,
Myotis lucifugus	ENSMLUG00000000745	5 retrocopies	retro_mluc_1961, retro_mluc_2533, retro_mluc_2570, retro_mluc_2617, retro_mluc_2622,
Macaca mulatta	ENSMMUG00000009939	1 retrocopy	retro_mmul_1915,
Monodelphis domestica	ENSMODG00000017419	2 retrocopies	retro_mdom_400, retro_mdom_901,
Mus musculus	ENSMUSG00000057572	1 retrocopy	retro_mmus_2631,
Oryctolagus cuniculus	ENSOCUG00000000940	1 retrocopy	retro_ocun_492,
Otolemur garnettii	ENSOGAG00000011630	1 retrocopy	retro_ogar_3231,
Pongo abelii	ENSPPYG00000001589	2 retrocopies	retro_pabe_13, retro_pabe_2478,
Tursiops truncatus	ENSTTRG00000014968	1 retrocopy	retro_ttru_1200,