RetrogeneDB ID: retro_ecab_231

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:13097454..13097898(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000007695
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FUNDC1
• Ensembl ID: ENSECAG00000022709
• Aliases: None
• Description: FUN14 domain containing 1 [Source:HGNC Symbol;Acc:28746]

Sequence

>retro_ecab_231
CCTGAAGAACATGAAACTGATGATGACTCTTCTGAAATGTTGGACTTAAGTGAGTAGGCAAGAAGACACCATTGGTGGAA
TCGAGTGTTTGTCTATAATTTCAAACCTATGGTAGAAAAAATACTCAGTAGCCACTCAGATTATTATGGGTGGAGTGACT
GACTGGTGTGTGGGGTTTTTGTTCCAGAAGGTTGAAAAGCTTGCAGCAACTGCAGTAGACGGTGGCTTTCTTCTCATTCA
GATTGCCAGTCTCAGTGGCTATGTGCAGATCGACTGGAAGAGAGGTGAAAAAGATGTAAACAAAGCAAAAAGACATTTAA
GAAATGAGCAAATAAAGCAGCACCAGAATTCAACAAGATAATTGAAGAAGCAACAGAATTTGTTAAACAAAACATTGTGA
TATCCAGTGGATTTGTGGTAGGCTTTTGGCTAGGACTTACATCT

Alignment

ORF - retro_ecab_231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 95.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PQEYESDDDSYEVLDLTEYARRHHWWNRVFGHSSGPMVEK-YSVATQIVMGGVTGWCAGFLFQKVGKLAA
          P.E.E.DDDS.E.LDL.E.ARRHHWWNRVF.....PMVEK.YSVATQI.MGGVT.WC.GFLFQKV.KLAA
Retrocopy PEEHETDDDSSEMLDLSE*ARRHHWWNRVFVYNFKPMVEK>YSVATQIIMGGVTDWCVGFLFQKVEKLAA

Parental  TAVGGGFLLLQIASHSGYVQIDWKRVEKDVNKAKRQI-KKRANKAAPEINNIIEEATEFVKQNIVISSGF
          TAV.GGFLL.QIAS.SGYVQIDWKR.EKDVNKAKR...KK.ANKAAPE.N.IIEEATEFVKQNIVISSGF
Retrocopy TAVDGGFLLIQIASLSGYVQIDWKRGEKDVNKAKRHL<KK*ANKAAPEFNKIIEEATEFVKQNIVISSGF

Parental  VGGFLLGLAS
          V.GF.LGL.S
Retrocopy VVGFWLGLTS

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	6.85 RPM
SRP021940_cerebellum	0.00 RPM	17.45 RPM
SRP021940_embryo	0.08 RPM	6.29 RPM
SRP021940_placental_villous	0.00 RPM	3.42 RPM
SRP021940_synovial_membrane	0.00 RPM	4.69 RPM
SRP021940_testis	0.06 RPM	2.69 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_231 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_231 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_231 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010258	3 retrocopies	retro_amel_586, retro_amel_644, retro_amel_825,
Bos taurus	ENSBTAG00000001637	4 retrocopies	retro_btau_1370, retro_btau_1591, retro_btau_305, retro_btau_587,
Canis familiaris	ENSCAFG00000014506	3 retrocopies	retro_cfam_1269, retro_cfam_1675, retro_cfam_951,
Dasypus novemcinctus	ENSDNOG00000014551	2 retrocopies	retro_dnov_2091, retro_dnov_2240,
Equus caballus	ENSECAG00000022709	3 retrocopies	retro_ecab_210, retro_ecab_231 , retro_ecab_567,
Echinops telfairi	ENSETEG00000012763	3 retrocopies	retro_etel_1614, retro_etel_697, retro_etel_852,
Felis catus	ENSFCAG00000005541	3 retrocopies	retro_fcat_1493, retro_fcat_179, retro_fcat_205,
Latimeria chalumnae	ENSLACG00000010215	1 retrocopy	retro_lcha_74,
Macropus eugenii	ENSMEUG00000006795	5 retrocopies	retro_meug_1597, retro_meug_2127, retro_meug_232, retro_meug_415, retro_meug_994,
Myotis lucifugus	ENSMLUG00000015860	3 retrocopies	retro_mluc_1032, retro_mluc_2302, retro_mluc_2304,
Macaca mulatta	ENSMMUG00000003505	1 retrocopy	retro_mmul_38,
Monodelphis domestica	ENSMODG00000021088	3 retrocopies	retro_mdom_1262, retro_mdom_769, retro_mdom_917,
Mustela putorius furo	ENSMPUG00000012924	1 retrocopy	retro_mputfur_209,
Oryctolagus cuniculus	ENSOCUG00000029753	5 retrocopies	retro_ocun_1008, retro_ocun_1376, retro_ocun_1567, retro_ocun_27, retro_ocun_314,
Pelodiscus sinensis	ENSPSIG00000013793	1 retrocopy	retro_psin_30,
Pteropus vampyrus	ENSPVAG00000009327	2 retrocopies	retro_pvam_1380, retro_pvam_232,
Sorex araneus	ENSSARG00000012878	4 retrocopies	retro_sara_276, retro_sara_367, retro_sara_494, retro_sara_551,
Sarcophilus harrisii	ENSSHAG00000000501	1 retrocopy	retro_shar_222,
Tursiops truncatus	ENSTTRG00000010466	2 retrocopies	retro_ttru_1099, retro_ttru_1735,