RetrogeneDB ID: retro_ecab_341

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:88054484..88054977(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS27A
• Ensembl ID: ENSECAG00000018773
• Aliases: None
• Description: ribosomal protein S27a [Source:HGNC Symbol;Acc:10417]

Sequence

>retro_ecab_341
TTTCCAATCATCATCTGCGCTGGAAGCATCACCAAGATGAAGATATTTGTAAAACCTTTAGGGGAAGCCCATCATTCTTG
AGGTGGAAACATTGGATACAATAAAAAATGTAAAGGCCAAGATCCAGGATGAGGAAGGACTCTCTCTCGATCAGCAAAGA
CTGATCTTACTGGCAAGAAACTGGAGATGGACATGCTTTGCCTGACTGTAGCATTCAAAGGAGTCCACTGTTTACCTTGT
GTTGAGACTGTGGTGGAACTAAGAAAAGGAGGAAGTCTTATACCACTCCCAAGAAGAATAAGCATAAGAAAAAGAAGTTT
AAGCTGGCTGGCCTGAAATACTACAAGGTGAATGAGAATGGCAAAATTAGTCTCCTTTGTTGGGAGTGCTCCTCAGATAA
ATGTGGTGCTGGAATTTTATGGCCAGCCACTTTGACAGATGTTATTATGACAAATGTTGCTTTACCTATTGTTTCAATAA
ACCAGAAGACAAG

Alignment

ORF - retro_ecab_341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.9 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FQSAICGATAAKMQIFV-KT-LTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF-AGKQLE-DGR
          F...IC.....KM.IFV.KT.L.GK.I.LEVE..DTI.NVKAKIQD.EG...DQQRLI...GK.LE.DG.
Retrocopy FPIIICAGSITKMKIFV<KT<L*GKPIILEVETLDTIKNVKAKIQDEEGLSLDQQRLIL<TGKKLE<DGH

Parental  TLSDYNIQKESTLHLVLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSD
          .L.D..IQ..S.L.......GG.KKR..KSYTTPKKNKHK.KK.KLA.LKYYKV.ENGKIS.L..EC.SD
Retrocopy ALPDCSIQR-SPLFTLC*DCGGTKKRR-KSYTTPKKNKHKKKKFKLAGLKYYKVNENGKISLLCWECSSD

Parental  ECGAGV-FMASHFDRHYCGKCCLTYCFNKPEDK
          .CGAG..FMASHFDR.Y..KCC.TYCFNKPEDK
Retrocopy KCGAGI<FMASHFDRCYYDKCCFTYCFNKPEDK

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	230.63 RPM
SRP021940_cerebellum	0.00 RPM	101.84 RPM
SRP021940_embryo	0.00 RPM	161.95 RPM
SRP021940_placental_villous	0.00 RPM	153.91 RPM
SRP021940_synovial_membrane	0.03 RPM	144.48 RPM
SRP021940_testis	0.06 RPM	70.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_341 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_341 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_341 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004017	5 retrocopies	retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Canis familiaris	ENSCAFG00000023471	3 retrocopies	retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus	ENSCJAG00000010052	5 retrocopies	retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Equus caballus	ENSECAG00000018773	3 retrocopies	retro_ecab_341 , retro_ecab_748, retro_ecab_776,
Gorilla gorilla	ENSGGOG00000007678	9 retrocopies	retro_ggor_1290, retro_ggor_1291, retro_ggor_1502, retro_ggor_1749, retro_ggor_179, retro_ggor_203, retro_ggor_2373, retro_ggor_2858, retro_ggor_2885,
Loxodonta africana	ENSLAFG00000023133	2 retrocopies	retro_lafr_1122, retro_lafr_185,
Myotis lucifugus	ENSMLUG00000017064	10 retrocopies	retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus	ENSMLUG00000029449	1 retrocopy	retro_mluc_1585,
Macaca mulatta	ENSMMUG00000015563	8 retrocopies	retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica	ENSMODG00000001819	3 retrocopies	retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Oryctolagus cuniculus	ENSOCUG00000003613	10 retrocopies	retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Pongo abelii	ENSPPYG00000025871	1 retrocopy	retro_pabe_117,
Pan troglodytes	ENSPTRG00000011928	1 retrocopy	retro_ptro_32,
Rattus norvegicus	ENSRNOG00000004426	2 retrocopies	retro_rnor_117, retro_rnor_161,
Ictidomys tridecemlineatus	ENSSTOG00000009566	5 retrocopies	retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,