RetrogeneDB ID: retro_ecab_1115

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:60753332..60753736(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000011121
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000007201
• Aliases: None
• Description: None

Sequence

>retro_ecab_1115
ATGGCTGCCCTCAGACCCCTCGTGAAGCCCAAGATCGTCAAAAAGAGGACCAAGAAGTTCATTCGGCACCAGTCAGACTG
ATATGTCAAAATTAAGCGTAACTGGCGGAAACCCAGAGGCATTGACAATAGGGTGCGCAGAAGATTCAAGGGCCAGATCT
TGATGCCCAACATTGGTTATGGGAGCAATAAGAAAACGAAGCACATGCTGCCCAGTGGCTTCCGGAAGTTCCTGGTCCAC
AACGTCAAGGAGCTTGAAGTGCTGCTCATGTGCAACAAATCGTACTGTGCTGAGATTGCTCACGACGTCTCCTCCAAGAA
CCGCAAAGCCATCGTGGAAAGAGCAGCCCAGCTGGCCATCAGAATCACCAATCCCAATGCCAGCTGCGCAGCGAAGAAAA
CGAA

Alignment

ORF - retro_ecab_1115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHML
          MAALRPLVKPKIVKKRTKKFIRHQSD.YVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHML
Retrocopy MAALRPLVKPKIVKKRTKKFIRHQSD*YVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHML

Parental  PSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRITNPNA-RLRSEENE
          PSGFRKFLVHNVKELEVLLMCNKSYCAEIAH.VSSKNRKAIVERAAQLAIRITNPNA..LRSEENE
Retrocopy PSGFRKFLVHNVKELEVLLMCNKSYCAEIAHDVSSKNRKAIVERAAQLAIRITNPNA<QLRSEENE

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	0.71 RPM	133.35 RPM
SRP021940_cerebellum	0.42 RPM	45.44 RPM
SRP021940_embryo	1.05 RPM	97.07 RPM
SRP021940_placental_villous	0.48 RPM	63.27 RPM
SRP021940_synovial_membrane	0.82 RPM	93.34 RPM
SRP021940_testis	0.38 RPM	44.95 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1115 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1115 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 239 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014763	3 retrocopies	retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca	ENSAMEG00000004583	26 retrocopies	retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Bos taurus	ENSBTAG00000015283	10 retrocopies	retro_btau_1102, retro_btau_1391, retro_btau_1568, retro_btau_1645, retro_btau_1728, retro_btau_1764, retro_btau_377, retro_btau_623, retro_btau_631, retro_btau_654,
Choloepus hoffmanni	ENSCHOG00000013534	27 retrocopies	retro_chof_1131, retro_chof_1164, retro_chof_1181, retro_chof_1234, retro_chof_1461, retro_chof_152, retro_chof_1821, retro_chof_1957, retro_chof_2022, retro_chof_205, retro_chof_2090, retro_chof_2146, retro_chof_2242, retro_chof_2265, retro_chof_2301, retro_chof_2410, retro_chof_2509, retro_chof_2527, retro_chof_2606, retro_chof_276, retro_chof_286, retro_chof_313, retro_chof_554, retro_chof_585, retro_chof_607, retro_chof_758, retro_chof_913,
Cavia porcellus	ENSCPOG00000019967	2 retrocopies	retro_cpor_1241, retro_cpor_608,
Dipodomys ordii	ENSDORG00000008426	6 retrocopies	retro_dord_175, retro_dord_251, retro_dord_371, retro_dord_458, retro_dord_522, retro_dord_664,
Equus caballus	ENSECAG00000007201	4 retrocopies	retro_ecab_1115 , retro_ecab_26, retro_ecab_369, retro_ecab_698,
Erinaceus europaeus	ENSEEUG00000011609	5 retrocopies	retro_eeur_161, retro_eeur_247, retro_eeur_300, retro_eeur_39, retro_eeur_576,
Felis catus	ENSFCAG00000030450	38 retrocopies	retro_fcat_1014, retro_fcat_1063, retro_fcat_1173, retro_fcat_1185, retro_fcat_1186, retro_fcat_1340, retro_fcat_1402, retro_fcat_144, retro_fcat_1515, retro_fcat_1526, retro_fcat_16, retro_fcat_1600, retro_fcat_1620, retro_fcat_1665, retro_fcat_1674, retro_fcat_1779, retro_fcat_1819, retro_fcat_1847, retro_fcat_1857, retro_fcat_1863, retro_fcat_191, retro_fcat_1912, retro_fcat_1981, retro_fcat_319, retro_fcat_357, retro_fcat_412, retro_fcat_435, retro_fcat_438, retro_fcat_499, retro_fcat_510, retro_fcat_660, retro_fcat_740, retro_fcat_745, retro_fcat_893, retro_fcat_936, retro_fcat_95, retro_fcat_979, retro_fcat_997,
Homo sapiens	ENSG00000144713	20 retrocopies	retro_hsap_1013, retro_hsap_1115, retro_hsap_1547, retro_hsap_1789, retro_hsap_1956, retro_hsap_2618, retro_hsap_2821, retro_hsap_2891, retro_hsap_3024, retro_hsap_3450, retro_hsap_3536, retro_hsap_3582, retro_hsap_3726, retro_hsap_3805, retro_hsap_3936, retro_hsap_3982, retro_hsap_4008, retro_hsap_4155, retro_hsap_4677, retro_hsap_814,
Loxodonta africana	ENSLAFG00000032737	1 retrocopy	retro_lafr_14,
Myotis lucifugus	ENSMLUG00000022528	6 retrocopies	retro_mluc_100, retro_mluc_1283, retro_mluc_173, retro_mluc_2224, retro_mluc_2256, retro_mluc_48,
Macaca mulatta	ENSMMUG00000001340	6 retrocopies	retro_mmul_106, retro_mmul_117, retro_mmul_126, retro_mmul_79, retro_mmul_93, retro_mmul_95,
Mustela putorius furo	ENSMPUG00000017189	4 retrocopies	retro_mputfur_121, retro_mputfur_76, retro_mputfur_8, retro_mputfur_85,
Mus musculus	ENSMUSG00000057841	16 retrocopies	retro_mmus_1132, retro_mmus_1142, retro_mmus_1746, retro_mmus_2010, retro_mmus_2263, retro_mmus_2316, retro_mmus_2341, retro_mmus_2699, retro_mmus_3099, retro_mmus_3378, retro_mmus_3605, retro_mmus_385, retro_mmus_442, retro_mmus_496, retro_mmus_533, retro_mmus_985,
Nomascus leucogenys	ENSNLEG00000004789	12 retrocopies	retro_nleu_1109, retro_nleu_125, retro_nleu_1452, retro_nleu_1642, retro_nleu_193, retro_nleu_224, retro_nleu_2808, retro_nleu_2809, retro_nleu_442, retro_nleu_497, retro_nleu_56, retro_nleu_603,
Otolemur garnettii	ENSOGAG00000028498	24 retrocopies	retro_ogar_129, retro_ogar_1321, retro_ogar_1340, retro_ogar_1360, retro_ogar_1425, retro_ogar_1524, retro_ogar_160, retro_ogar_1683, retro_ogar_1766, retro_ogar_1833, retro_ogar_2032, retro_ogar_2412, retro_ogar_2416, retro_ogar_2515, retro_ogar_3247, retro_ogar_3384, retro_ogar_545, retro_ogar_56, retro_ogar_571, retro_ogar_776, retro_ogar_870, retro_ogar_891, retro_ogar_924, retro_ogar_973,
Pongo abelii	ENSPPYG00000013391	2 retrocopies	retro_pabe_135, retro_pabe_98,
Rattus norvegicus	ENSRNOG00000010746	4 retrocopies	retro_rnor_179, retro_rnor_27, retro_rnor_278, retro_rnor_327,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,
Sus scrofa	ENSSSCG00000027637	9 retrocopies	retro_sscr_1001, retro_sscr_1054, retro_sscr_107, retro_sscr_1081, retro_sscr_165, retro_sscr_76, retro_sscr_793, retro_sscr_957, retro_sscr_989,
Ictidomys tridecemlineatus	ENSSTOG00000026505	9 retrocopies	retro_itri_1294, retro_itri_1322, retro_itri_1465, retro_itri_1639, retro_itri_1715, retro_itri_1748, retro_itri_370, retro_itri_885, retro_itri_948,
Tupaia belangeri	ENSTBEG00000012875	3 retrocopies	retro_tbel_3304, retro_tbel_47, retro_tbel_51,
Vicugna pacos	ENSVPAG00000002594	1 retrocopy	retro_vpac_17,