RetrogeneDB ID: retro_ecab_289

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:31392789..31393201(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL27A
• Ensembl ID: ENSECAG00000022469
• Aliases: None
• Description: ribosomal protein L27a [Source:HGNC Symbol;Acc:10329]

Sequence

>retro_ecab_289
AGACTGAGGGAGCCCTAGAAACTTCAGGGCCAGGTGAGCCATGGCGACAGCCACATCAGCAAGCACCAGAAGCACCCAGG
TAGCCGGGGCAATGCTGGTAGCAGGCATCACCACAGGAGCATCTTAGATAAATGCCACCCAGGTTACTTTGGCGAGGTTA
GCATAAGGCGTTACCACTTAAGGAGGAGTCAGAGCTTCTGCCCAACTGTCAATTTCGATGAATTACGGGCCTTGTTCAGT
GAGAAGACTTGGGTAAATGCTACCAAAAAACATGACTGGAGGTGCCCCCAACATGGATGTAGTGTAATGGAGCTAGGAAA
ACGGTCTAGGGAAGAGAAAGCTCCGAAAGCCACCTGTTATCATGAAGGTCGATTTCTTCAGCGGAAGAGCCAAGAAGAAT
AAGGACGGGGTA

Alignment

ORF - retro_ecab_289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.14 %
• Parental protein coverage: 93.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFCPTV
          RLR...KL.G.VSHG...I.KH.KHPG.RGNAG..HHHR...DK.HPGYFG.V..R.YHL.R.QSFCPTV
Retrocopy RLREP*KLQGQVSHGDSHISKHQKHPGSRGNAGSRHHHRSILDKCHPGYFGEVSIRRYHLRRSQSFCPTV

Parental  NLDKLWTLVSEQTRVNAA-KNKTGAAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGV
          N.D.L..L.SE.T.VNA..KN.TG.AP..DVV.......LGK.KL.K.PVI.K..FFS.RA.....GV
Retrocopy NFDELRALFSEKTWVNAT>KNMTGGAPNMDVV*WS*ENGLGKRKLRKPPVIMKVDFFSGRAKKNKDGV

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	642.89 RPM
SRP021940_cerebellum	0.00 RPM	315.59 RPM
SRP021940_embryo	0.00 RPM	458.93 RPM
SRP021940_placental_villous	0.00 RPM	308.92 RPM
SRP021940_synovial_membrane	0.00 RPM	405.08 RPM
SRP021940_testis	0.00 RPM	235.38 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_289 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004205	15 retrocopies	retro_amel_1095, retro_amel_1160, retro_amel_1165, retro_amel_130, retro_amel_1311, retro_amel_1441, retro_amel_1673, retro_amel_393, retro_amel_450, retro_amel_497, retro_amel_521, retro_amel_693, retro_amel_752, retro_amel_966, retro_amel_989,
Bos taurus	ENSBTAG00000005349	2 retrocopies	retro_btau_126, retro_btau_45,
Canis familiaris	ENSCAFG00000006936	2 retrocopies	retro_cfam_145, retro_cfam_384,
Callithrix jacchus	ENSCJAG00000011775	1 retrocopy	retro_cjac_211,
Equus caballus	ENSECAG00000022469	1 retrocopy	retro_ecab_289 ,
Felis catus	ENSFCAG00000008411	13 retrocopies	retro_fcat_1162, retro_fcat_1285, retro_fcat_1305, retro_fcat_1380, retro_fcat_1635, retro_fcat_1761, retro_fcat_1805, retro_fcat_1974, retro_fcat_469, retro_fcat_652, retro_fcat_673, retro_fcat_817, retro_fcat_907,
Loxodonta africana	ENSLAFG00000000425	2 retrocopies	retro_lafr_25, retro_lafr_50,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Oryctolagus cuniculus	ENSOCUG00000005442	1 retrocopy	retro_ocun_12,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Sus scrofa	ENSSSCG00000014569	9 retrocopies	retro_sscr_527, retro_sscr_574, retro_sscr_587, retro_sscr_588, retro_sscr_644, retro_sscr_668, retro_sscr_677, retro_sscr_769, retro_sscr_809,