RetrogeneDB ID: retro_ecab_200

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:175105924..175106163(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTF3
• Ensembl ID: ENSECAG00000021629
• Aliases: None
• Description: basic transcription factor 3 [Source:HGNC Symbol;Acc:1125]

Sequence

>retro_ecab_200
CAGGAATCTCTGGCAGCCAACATCTTCACCATTACAGGCCATGCTGGGACAAAGCTGCCGACAGAAATGCCAGCAGCATC
TGAAACCAGCTTGGTGCAGACAGTGACTGGTTTAAGGAGACTGGCTGAAGCTCTGCCCAAATAATCTGTGGATGGGAAAC
CCTGCTTGCCACTGGAGAGGAGGATGAAGTTTCAGATCTTGTGCAGAATGGTGCTGAGGCTTCCAGGAAGGAAGCAAAT

Alignment

ORF - retro_ecab_200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 50.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRRLAEALPKQSVDGK-APLATGEEDDDEVPD
          Q.SLAAN.FTITGHA.TK..TEM.P...........T.LRRLAEALPK.SVDGK...LATGEE..DEV.D
Retrocopy QESLAANIFTITGHAGTKLPTEM-PAASETSLVQTVTGLRRLAEALPK*SVDGK<TLLATGEE--DEVSD

Parental  LVENFDEASKNEAN
          LV.N..EAS..EAN
Retrocopy LVQNGAEASRKEAN

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	192.67 RPM
SRP021940_cerebellum	0.00 RPM	82.83 RPM
SRP021940_embryo	0.00 RPM	201.79 RPM
SRP021940_placental_villous	0.00 RPM	132.11 RPM
SRP021940_synovial_membrane	0.00 RPM	158.40 RPM
SRP021940_testis	0.00 RPM	213.89 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_200 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_200 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 94 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011563	14 retrocopies	retro_amel_1257, retro_amel_1279, retro_amel_1324, retro_amel_1334, retro_amel_1433, retro_amel_166, retro_amel_1769, retro_amel_182, retro_amel_1841, retro_amel_480, retro_amel_513, retro_amel_784, retro_amel_908, retro_amel_986,
Bos taurus	ENSBTAG00000010012	5 retrocopies	retro_btau_1161, retro_btau_1344, retro_btau_1361, retro_btau_459, retro_btau_551,
Canis familiaris	ENSCAFG00000008212	3 retrocopies	retro_cfam_1660, retro_cfam_1741, retro_cfam_531,
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Cavia porcellus	ENSCPOG00000012832	1 retrocopy	retro_cpor_81,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Equus caballus	ENSECAG00000021629	1 retrocopy	retro_ecab_200 ,
Echinops telfairi	ENSETEG00000017341	5 retrocopies	retro_etel_1216, retro_etel_1394, retro_etel_1997, retro_etel_405, retro_etel_960,
Felis catus	ENSFCAG00000023973	10 retrocopies	retro_fcat_1044, retro_fcat_1378, retro_fcat_1438, retro_fcat_187, retro_fcat_188, retro_fcat_225, retro_fcat_28, retro_fcat_419, retro_fcat_593, retro_fcat_919,
Gorilla gorilla	ENSGGOG00000000166	10 retrocopies	retro_ggor_1082, retro_ggor_1682, retro_ggor_1961, retro_ggor_2054, retro_ggor_2399, retro_ggor_2647, retro_ggor_2667, retro_ggor_548, retro_ggor_81, retro_ggor_946,
Myotis lucifugus	ENSMLUG00000012912	11 retrocopies	retro_mluc_1024, retro_mluc_1349, retro_mluc_1459, retro_mluc_1748, retro_mluc_1820, retro_mluc_1823, retro_mluc_2560, retro_mluc_2602, retro_mluc_482, retro_mluc_682, retro_mluc_694,
Macaca mulatta	ENSMMUG00000022291	2 retrocopies	retro_mmul_105, retro_mmul_2424,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Otolemur garnettii	ENSOGAG00000013918	1 retrocopy	retro_ogar_46,
Pongo abelii	ENSPPYG00000029576	14 retrocopies	retro_pabe_1154, retro_pabe_1477, retro_pabe_180, retro_pabe_1885, retro_pabe_1956, retro_pabe_2207, retro_pabe_2458, retro_pabe_2918, retro_pabe_2919, retro_pabe_2932, retro_pabe_3329, retro_pabe_3484, retro_pabe_558, retro_pabe_649,
Rattus norvegicus	ENSRNOG00000016912	9 retrocopies	retro_rnor_187, retro_rnor_194, retro_rnor_2121, retro_rnor_2520, retro_rnor_2990, retro_rnor_2991, retro_rnor_2999, retro_rnor_836, retro_rnor_953,