RetrogeneDB ID: retro_ecab_328

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:39329475..39329823(+)
• Located in intron of: ENSECAG00000016963

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS20
• Ensembl ID: ENSECAG00000012463
• Aliases: None
• Description: ribosomal protein S20 [Source:HGNC Symbol;Acc:10405]

Sequence

>retro_ecab_328
GCTTTGAAAGATATCAGAAAGACACCTACGGAACCAGAGGTGGCGATTCATCAAATGAGAATCACCCTAACTAGTGACAG
TGTAAGACCTCTGGAGAAGGTGTGTGCTGACTTGATCCGAGGCACAAAAGAAAATCTCAAAGTGAAAGGACCAGGTGGGA
GGCCTATCGAGACTCTGGGAATCACTAAAAGAAAAACTCTTTGTGCTGTAAGGTTCTTAGACTTGGGATTTTTTCAGATC
AGTATCTACGAGTGACTCACTACCTTGGACAGTCCTTCTGAGATTGTTAAGCAGATTACTTCCATCAGTATTTAGCCAGG
AGAAGAGGCTCAAGTCACCAGTGCAGAT

Alignment

ORF - retro_ecab_328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.23 %
• Parental protein coverage: 98.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPCG
          A.KD..KTP.EPEVAIH..RITLTS..V..LEKVCADLIRG.KE.NLKVKGP...P..TL.IT.RKT.C.
Retrocopy ALKDIRKTPTEPEVAIHQMRITLTSDSVRPLEKVCADLIRGTKE-NLKVKGPGGRPIETLGITKRKTLCA

Parental  E-GSKTWDRF-QMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIAD
          ..GS.TWD.F.Q..I...L..L.SPSEIVKQITSISI.PG.E..VT.AD
Retrocopy V>GS*TWDFF<QISIYE*LTTLDSPSEIVKQITSISI*PGEEAQVTSAD

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	1033.26 RPM
SRP021940_cerebellum	0.00 RPM	272.96 RPM
SRP021940_embryo	0.15 RPM	669.95 RPM
SRP021940_placental_villous	0.05 RPM	345.97 RPM
SRP021940_synovial_membrane	0.19 RPM	524.77 RPM
SRP021940_testis	0.06 RPM	485.84 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_328 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_328 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_328 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 94 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012463	4 retrocopies	retro_ecab_328 , retro_ecab_378, retro_ecab_536, retro_ecab_573,
Echinops telfairi	ENSETEG00000003394	3 retrocopies	retro_etel_16, retro_etel_1814, retro_etel_2067,
Macropus eugenii	ENSMEUG00000014171	21 retrocopies	retro_meug_100, retro_meug_1015, retro_meug_1058, retro_meug_1170, retro_meug_1313, retro_meug_1614, retro_meug_1702, retro_meug_1761, retro_meug_1777, retro_meug_1831, retro_meug_1911, retro_meug_1951, retro_meug_2065, retro_meug_2110, retro_meug_2187, retro_meug_659, retro_meug_710, retro_meug_723, retro_meug_818, retro_meug_892, retro_meug_928,
Monodelphis domestica	ENSMODG00000009114	6 retrocopies	retro_mdom_1701, retro_mdom_1735, retro_mdom_1738, retro_mdom_1814, retro_mdom_1817, retro_mdom_1943,
Mustela putorius furo	ENSMPUG00000010452	15 retrocopies	retro_mputfur_1094, retro_mputfur_1188, retro_mputfur_1313, retro_mputfur_1366, retro_mputfur_1374, retro_mputfur_1432, retro_mputfur_238, retro_mputfur_249, retro_mputfur_320, retro_mputfur_418, retro_mputfur_424, retro_mputfur_433, retro_mputfur_620, retro_mputfur_77, retro_mputfur_819,
Nomascus leucogenys	ENSNLEG00000001214	19 retrocopies	retro_nleu_1013, retro_nleu_1343, retro_nleu_1447, retro_nleu_1566, retro_nleu_1794, retro_nleu_1798, retro_nleu_1805, retro_nleu_1818, retro_nleu_2059, retro_nleu_2159, retro_nleu_2654, retro_nleu_2659, retro_nleu_2750, retro_nleu_2786, retro_nleu_2819, retro_nleu_2843, retro_nleu_3066, retro_nleu_382, retro_nleu_41,
Rattus norvegicus	ENSRNOG00000008555	7 retrocopies	retro_rnor_142, retro_rnor_155, retro_rnor_192, retro_rnor_288, retro_rnor_381, retro_rnor_401, retro_rnor_58,
Sarcophilus harrisii	ENSSHAG00000011200	10 retrocopies	retro_shar_135, retro_shar_228, retro_shar_418, retro_shar_436, retro_shar_441, retro_shar_443, retro_shar_450, retro_shar_504, retro_shar_544, retro_shar_785,
Tursiops truncatus	ENSTTRG00000016847	9 retrocopies	retro_ttru_1206, retro_ttru_1257, retro_ttru_1850, retro_ttru_1935, retro_ttru_350, retro_ttru_422, retro_ttru_434, retro_ttru_48, retro_ttru_570,