RetrogeneDB ID: retro_ecab_628

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 24:11343111..11344650(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA8
• Ensembl ID: ENSECAG00000013510
• Aliases: None
• Description: Heat shock cognate 71 kDa protein [Source:UniProtKB/Swiss-Prot;Acc:A2Q0Z1]

Sequence

>retro_ecab_628
CCCGAGGAGATCTCCTCCATGGTCCTCACTAAGATGAAGGAGATCGCCGAAGCCTACCTGGGGGGCAAAGTGCAGAGCGC
GGTCATCACCGTCCCGGCCTATTTCAACGACTCGCAGCGCCAGGCCACCAAGGACGCGGGCACCATCACCGGCCTCAACG
TGCTGCGCATCATCAACGAGCCCACGGCGGCGGCCATCGCCTACGGCCTGGACAAGAAGGGCTGCACGGGCGGCGAGAAG
AACGTGCTCATCTTTGACCTGGGCGGCGGCACCTTCGACGTGTCCATCCTGACCATCGAGGACGGCATCTTCGAGGTGAA
GTCCACGGCCGGCGACACCCACCTGGGCGGCGAGGACTTTGACAACCGCATGGTGAGCCATCTGGCGGAGGAGTTCAAGC
GCAAGCACAAGAAGGACATCGCGCCCAACAAGCGCGCGGTGCGGCGGCTGCGCACGGCCTGCGAGCGCGCCAAGCGCACC
CTGAGCTCGTCCACGCAGGCGAGCATCGAGATCGACTCGCTCTACGAGGGCGTGGACTTCTACACGTCCATCACCCGCGC
CCGCTTCGAGGAGCTCAACGCCGACCTGTTCCGCGGGACCCTGGAGCCGGTGGAGAAGGCGCTGCGCGACGCCAAGCTGG
ACAAGGGCCAGATCCAGGAGATCGTGCTGGTGGGCGGCTCTACCCGCATCCCCAAGATTCAGAAGCTGCTGCAGGATTTC
TTCAATGGCAAGGAGCTGAACAAGAGCATCAACCCCGACGAGGCGGTGGCCTACGGAGCCGCGGTACAGGCAGCCATCCT
CATCGGGGACAAGTCAGAGAACGTGCAGGACCTGCTGCTACTCGACGTGACCCCGTTGTCCCTGGGCATCGAGACGGCTG
GCGGCGTCATGACCCCACTCATCAAGAGGAACACCACGATCCCCACCAAGCAGACGCAGACCTTCACCACTTACTCAGAC
AACCAGAGCAGCGTGCTGGTGCAGGTGTACGAGGGCGAACGGGCCATGACCAAGGACAATAACCTGCTGGGCAAGTTCGA
CCTGACCGGGATTCCCCCGGCGCCCCGCGGCGTCCCCCAGATCGAGGTCACCTTCGACATCGACGCCAACGGCATCCTCA
ACGTCACCGCCGCCGACAAGAGCACCGGTAAAGAAAACAAAATCACCATCACCAACGATAAGGGTCGTCTGAGCAAGGAC
GACATTGACCGGATGGTGCAGGAGGCGGAGCGGTACAAGTCGGAAGATGAGGCCAATCGCGACCGGGTCGCGGCCAAAAA
CGCCGTGGAGTCCTATACCTACAACATCAAGCAGACGGTGGAAGACGAGAAACTGAGGGGCAAGATTAGCGACCAGGACA
AAAACAAGATCCTCGACAAGTGTCAGGAGGTGATCAACTGGCTCGACCGAAACCAGATGGCAGAGAAAGATGAGTATGAA
CACAAGCAGAAAGAGCTTGAAAGAGTGTGCAACCCCATCATCAGCAAACTTTACCAAGGCGGCCCTGGCGGCGGCGGCGG
TTCTGGAGCCTCCGGGGGA

Alignment

ORF - retro_ecab_628 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.8 %
• Parental protein coverage: 79.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGL
          PEE.SSMVLTKMKEIAEAYLG..V..AV.TVPAYFNDSQRQATKDAGTI.GLNVLRIINEPTAAAIAYGL
Retrocopy PEEISSMVLTKMKEIAEAYLGGKVQSAVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGL

Parental  DKK--VGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDI
          DKK...G.E.NVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMV.H...EFKRKHKKDI
Retrocopy DKKGCTGGEKNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDI

Parental  SENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRD
          ..NKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEG.DFYTSITRARFEELNADLFRGTL.PVEKALRD
Retrocopy APNKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRD

Parental  AKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLL
          AKLDK.QI..IVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAIL.GDKSENVQDLLL
Retrocopy AKLDKGQIQEIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILIGDKSENVQDLLL

Parental  LDVTPLSLGIETAGGVMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTG
          LDVTPLSLGIETAGGVMT.LIKRNTTIPTKQTQTFTTYSDNQ..VL.QVYEGERAMTKDNNLLGKF.LTG
Retrocopy LDVTPLSLGIETAGGVMTPLIKRNTTIPTKQTQTFTTYSDNQSSVLVQVYEGERAMTKDNNLLGKFDLTG

Parental  IPPAPRGVPQIEVTFDIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQR
          IPPAPRGVPQIEVTFDIDANGILNV.A.DKSTGKENKITITNDKGRLSK.DI.RMVQEAE.YK.EDE..R
Retrocopy IPPAPRGVPQIEVTFDIDANGILNVTAADKSTGKENKITITNDKGRLSKDDIDRMVQEAERYKSEDEANR

Parental  DKVSSKNSLESYAFNMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVC
          D.V..KN..ESY..N.K.TVEDEKL.GKI.D.DK.KILDKC.E.INWLD.NQ.AEK.E.EH.QKELE.VC
Retrocopy DRVAAKNAVESYTYNIKQTVEDEKLRGKISDQDKNKILDKCQEVINWLDRNQMAEKDEYEHKQKELERVC

Parental  NPIITKLYQSAGGMPGGMPGGFPGG
          NPII.KLYQ..GG..GG...G..GG
Retrocopy NPIISKLYQ--GGPGGGGGSGASGG

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	120.24 RPM	93.27 RPM
SRP021940_cerebellum	171.53 RPM	421.85 RPM
SRP021940_embryo	23.76 RPM	381.14 RPM
SRP021940_placental_villous	126.15 RPM	399.85 RPM
SRP021940_synovial_membrane	13.64 RPM	245.97 RPM
SRP021940_testis	1481.69 RPM	210.82 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_ecab_628 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CX595813	11343651	11344126	100	475	0	475

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_628 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_628 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_53

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004884	2 retrocopies	retro_acar_21, retro_acar_6,
Anas platyrhynchos	ENSAPLG00000010667	1 retrocopy	retro_apla_6,
Canis familiaris	ENSCAFG00000011666	3 retrocopies	retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis	ENSCING00000009665	1 retrocopy	retro_cint_12,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Equus caballus	ENSECAG00000013510	2 retrocopies	retro_ecab_291, retro_ecab_628 ,
Echinops telfairi	ENSETEG00000010996	1 retrocopy	retro_etel_43,
Ficedula albicollis	ENSFALG00000005812	1 retrocopy	retro_falb_18,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
Loxodonta africana	ENSLAFG00000030312	4 retrocopies	retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo	ENSMGAG00000001929	1 retrocopy	retro_mgal_9,
Myotis lucifugus	ENSMLUG00000004834	3 retrocopies	retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica	ENSMODG00000012958	2 retrocopies	retro_mdom_127, retro_mdom_99,
Mustela putorius furo	ENSMPUG00000005810	9 retrocopies	retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Nomascus leucogenys	ENSNLEG00000007419	8 retrocopies	retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Ictidomys tridecemlineatus	ENSSTOG00000003756	1 retrocopy	retro_itri_51,
Taeniopygia guttata	ENSTGUG00000000491	1 retrocopy	retro_tgut_7,
Takifugu rubripes	ENSTRUG00000005265	1 retrocopy	retro_trub_30,
Xiphophorus maculatus	ENSXMAG00000001602	1 retrocopy	retro_xmac_20,