RetrogeneDB ID: retro_ecab_429

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:30422302..30422720(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000015757
• Aliases: None
• Description: None

Sequence

>retro_ecab_429
TTCACGTCTTCTGATCAGAACAAGAACCACGAAAGGCATTTCAACGCACCTTCCCACATTTGCAGGAAGATTATGTCTTT
CCCTCTTTCCAAAGACCTGAGACAAAAGTACAATGTTTAATCCATGTCCATCTGAAAGGATGATAAGTTCAGGTTGTGTG
AGGACACTACAAAGGTCAGCAAATTGGCAAAGTAGTCCAAATTTACAGGAAGAAATGTGTCATCTACACTGAACTTGTGC
AGTGGGAGAAGCCAATGACACAACTGTCCATGTCGGCATGCAGCCCAGCAAAGTGGTTGTCACCAGGCTAAAACTGCACA
AAGATGGCAAAAAGATCCTTGAACATAAAACCAATTCTTGCCAAGTAGGGAAGGAAAAGAGCAAATATAAGGAAGAAACA
ATTGAGAAGATGTGGGAA

Alignment

ORF - retro_ecab_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.76 %
• Parental protein coverage: 96.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDE-VQVVRGHYKGQQIGKVVQVY
          F..SD..KN..RHFNAPSHI.RKIMS.PLSK.LRQKYNV.SM.I.KDD..VQVV.GHYKGQQIGKVVQ.Y
Retrocopy FTSSDQNKNHERHFNAPSHICRKIMSFPLSKDLRQKYNV*SMSI*KDDK<VQVV*GHYKGQQIGKVVQIY

Parental  RKKYVIYIERVQREK-ANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEETIEKM
          RKK.VIY.E.VQ.EK.AN.TTVHVG..PSKVV.TRLKL.KD.KKILE.K..S.QVGKEK.KYKEETIEKM
Retrocopy RKKCVIYTELVQWEK<ANDTTVHVGMQPSKVVVTRLKLHKDGKKILEHKTNSCQVGKEKSKYKEETIEKM

Parental  QE
          .E
Retrocopy WE

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	232.11 RPM
SRP021940_cerebellum	0.00 RPM	126.40 RPM
SRP021940_embryo	0.05 RPM	377.38 RPM
SRP021940_placental_villous	0.00 RPM	180.90 RPM
SRP021940_synovial_membrane	0.03 RPM	227.36 RPM
SRP021940_testis	0.00 RPM	106.79 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_429 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_429 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2165
Macaca mulatta	retro_mmul_903
Sus scrofa	retro_sscr_485

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 122 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002453	7 retrocopies	retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus	ENSBTAG00000012344	2 retrocopies	retro_btau_1090, retro_btau_230,
Callithrix jacchus	ENSCJAG00000014372	8 retrocopies	retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Equus caballus	ENSECAG00000015757	4 retrocopies	retro_ecab_429 , retro_ecab_473, retro_ecab_515, retro_ecab_609,
Felis catus	ENSFCAG00000011259	13 retrocopies	retro_fcat_1090, retro_fcat_1151, retro_fcat_1198, retro_fcat_1236, retro_fcat_1257, retro_fcat_1309, retro_fcat_1412, retro_fcat_1652, retro_fcat_1801, retro_fcat_1845, retro_fcat_1965, retro_fcat_497, retro_fcat_801,
Homo sapiens	ENSG00000161970	27 retrocopies	retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Gorilla gorilla	ENSGGOG00000023944	4 retrocopies	retro_ggor_2565, retro_ggor_270, retro_ggor_51, retro_ggor_974,
Myotis lucifugus	ENSMLUG00000002176	1 retrocopy	retro_mluc_232,
Macaca mulatta	ENSMMUG00000003448	22 retrocopies	retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica	ENSMODG00000006201	2 retrocopies	retro_mdom_36, retro_mdom_64,
Mustela putorius furo	ENSMPUG00000007988	12 retrocopies	retro_mputfur_1003, retro_mputfur_1146, retro_mputfur_1385, retro_mputfur_1428, retro_mputfur_1595, retro_mputfur_251, retro_mputfur_365, retro_mputfur_395, retro_mputfur_488, retro_mputfur_522, retro_mputfur_643, retro_mputfur_685,
Nomascus leucogenys	ENSNLEG00000009981	1 retrocopy	retro_nleu_76,
Otolemur garnettii	ENSOGAG00000017070	3 retrocopies	retro_ogar_118, retro_ogar_255, retro_ogar_66,
Pan troglodytes	ENSPTRG00000008742	3 retrocopies	retro_ptro_1546, retro_ptro_2510, retro_ptro_73,
Rattus norvegicus	ENSRNOG00000004214	3 retrocopies	retro_rnor_213, retro_rnor_260, retro_rnor_273,
Sarcophilus harrisii	ENSSHAG00000006890	1 retrocopy	retro_shar_458,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,