RetrogeneDB ID: retro_ecab_654

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 26:3114202..3115098(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL5
• Ensembl ID: ENSECAG00000021065
• Aliases: None
• Description: 60S ribosomal protein L5 [Source:RefSeq peptide;Acc:NP_001075354]

Sequence

>retro_ecab_654
CTGTTCTGCAGGATGGGGTTTGTCAAAGTTGCCAAGAATAAGGCCTACTGCAAGAGATACAAGTGAAATTTAGAAGACGA
CGAGAGGGTAAAACTGATTACTATGCTCAGAAACACTTAGTAATCCAGGATAAAAATAAGCACAACACACCCAAATACAG
GATGATAGTTCATGTAACCAACAGAGATGCCATTTGTCAGATGGCTTATGCCCGTATAGAAGGAGAGATGATAGTTTGTG
CAGCTTGTGCTCATGAACTCTTGGAGTTTGGCGCGAAGACTGGCCTCACACATTATGCATGCTGCCCTGGCCCGCTGCTG
GCCCACACGGTTCTCAATAGGTTTGGCATGGACAAGATCTGTGAAGGCCAAGTGGAGGTGACCGGAGAGGAACACAACGT
GGAAAGCATCGATGGTCAACCTGGTGCCTTCACCTGCTATTTGGATGTAGGGTTTGCCAGAACTACTACTGGAAATAAGG
TTTTTGGGGCCCTGAAAGGAGCTGTGGGTGGAGGCTTGTCTATACCTCACAGTACCAAACGATCCCCTAGTTATGATTCA
GAGAGCAAGGAATTCACTGCAGAAGTACAATGGAAGCACATCATGGGTCAGAACATTGCAGATTATATGTGTTACCTGGT
GGAAGAGGATGAGGATGCCTACAAGAAACAATTTTCTCAGTCCATAAAGAACAATGTAACTCCAGACTTGATGAAAGAGA
TGTGTAAGAAAGCTCATTCTGCTGTATGAGAGAATCCGGTCTATGCCAAGAAGCCTAAGAAAGAAGTTAAAAAGAAGAGG
TGGAACCGTCCCAAGATGTCTCTTGCCCAGAAGAAAGATTGGGTAGCTCAAAAGAAGGCAAGCTTCCTCAGAGCACAAGA
GCAGACCACTGAGAGC

Alignment

ORF - retro_ecab_654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.11 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFRRMGFVKVVKNKAYFKRY-QVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIA
          LF.RMGFVKV.KNKAY.KRY.QVKFRRRREGKTDYYA.K.LVIQDKNK.NTPKYRMIV.VTNRD.ICQ.A
Retrocopy LFCRMGFVKVAKNKAYCKRY<QVKFRRRREGKTDYYAQKHLVIQDKNKHNTPKYRMIVHVTNRDAICQMA

Parental  YARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESI
          YARIEG.MIVCAA.AHEL...G.K.GLT.YA...C.G.LLA...LNRFGMDKI.EGQVEVTG.E.NVESI
Retrocopy YARIEGEMIVCAACAHELLEFGAKTGLTHYAC--CPGPLLAHTVLNRFGMDKICEGQVEVTGEEHNVESI

Parental  DGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVA
          DGQPGAFTCYLD.G.ARTTTGNKVFGALKGAV.GGLSIPHSTKR.P.YDSESKEF.AEV..KHIMGQN.A
Retrocopy DGQPGAFTCYLDVGFARTTTGNKVFGALKGAVGGGLSIPHSTKRSPSYDSESKEFTAEVQWKHIMGQNIA

Parental  DYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHSAIRENPVYEKKPKKEVKKKRWNRPKMSLAQ
          DYM.YL.EEDEDAYKKQFSQ.IKNNVTPD.M.EM.KKAHSA..ENPVY.KKPKKEVKKKRWNRPKMSLAQ
Retrocopy DYMCYLVEEDEDAYKKQFSQSIKNNVTPDLMKEMCKKAHSAV*ENPVYAKKPKKEVKKKRWNRPKMSLAQ

Parental  KKDRVAQKKASFLRAQERAAES
          KKD.VAQKKASFLRAQE...ES
Retrocopy KKDWVAQKKASFLRAQEQTTES

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	0.47 RPM	1071.92 RPM
SRP021940_cerebellum	0.05 RPM	160.73 RPM
SRP021940_embryo	0.66 RPM	800.68 RPM
SRP021940_placental_villous	0.24 RPM	482.75 RPM
SRP021940_synovial_membrane	0.44 RPM	497.07 RPM
SRP021940_testis	0.19 RPM	159.41 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_654 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_654 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009878	5 retrocopies	retro_amel_1200, retro_amel_137, retro_amel_139, retro_amel_1439, retro_amel_1669,
Bos taurus	ENSBTAG00000002026	2 retrocopies	retro_btau_120, retro_btau_67,
Cavia porcellus	ENSCPOG00000000698	8 retrocopies	retro_cpor_1047, retro_cpor_1097, retro_cpor_1141, retro_cpor_1259, retro_cpor_1354, retro_cpor_1387, retro_cpor_428, retro_cpor_737,
Dipodomys ordii	ENSDORG00000005674	2 retrocopies	retro_dord_226, retro_dord_670,
Equus caballus	ENSECAG00000021065	1 retrocopy	retro_ecab_654 ,
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Mustela putorius furo	ENSMPUG00000004150	6 retrocopies	retro_mputfur_213, retro_mputfur_449, retro_mputfur_451, retro_mputfur_597, retro_mputfur_721, retro_mputfur_833,
Mus musculus	ENSMUSG00000058558	11 retrocopies	retro_mmus_1000, retro_mmus_1185, retro_mmus_1338, retro_mmus_1789, retro_mmus_1991, retro_mmus_2577, retro_mmus_2846, retro_mmus_297, retro_mmus_3076, retro_mmus_504, retro_mmus_911,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Oryctolagus cuniculus	ENSOCUG00000010089	2 retrocopies	retro_ocun_265, retro_ocun_54,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Pteropus vampyrus	ENSPVAG00000015117	4 retrocopies	retro_pvam_1427, retro_pvam_355, retro_pvam_505, retro_pvam_527,
Rattus norvegicus	ENSRNOG00000023529	6 retrocopies	retro_rnor_113, retro_rnor_2246, retro_rnor_2418, retro_rnor_2498, retro_rnor_2802, retro_rnor_2922,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,
Sus scrofa	ENSSSCG00000006899	2 retrocopies	retro_sscr_149, retro_sscr_219,
Tupaia belangeri	ENSTBEG00000010560	5 retrocopies	retro_tbel_101, retro_tbel_1054, retro_tbel_1518, retro_tbel_3006, retro_tbel_3530,
Tursiops truncatus	ENSTTRG00000013097	5 retrocopies	retro_ttru_1446, retro_ttru_1548, retro_ttru_1796, retro_ttru_645, retro_ttru_979,