RetrogeneDB ID: retro_ecab_1052

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:18542723..18544907(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004074
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUPT20H
• Ensembl ID: ENSECAG00000000116
• Aliases: None
• Description: suppressor of Ty 20 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20596]

Sequence

>retro_ecab_1052
ATGCAACACGCCTTAGAACGAGCTCTGGATCGCGCGGCGTGTGTCATCGAAAGTGCCCAACAGAGACCTCCTAAAAGGAA
GTACGCGTCTAGAGGGGAAAAATCGGTCTATGAGAAACTGTATGACATATATGTTGAAGAATGCGACAGAGAGCCTGAGG
TTGCGGAGGAATTACGAAGCAACGTGAACTTGCTAGAGAAGCTTGTTCAGAGAGAGTCGTTGTCGCGTTTAGTGGTCAAT
CTGCACCCAGGAGGGCAGGGATACTCGCTGATGCTCAGGGGAGAAAATGGCTCGTATTCGGAGACCATTCGGCTGTCTTA
TGAAGAGGGGGAACTGCTCCAGTACTTGGATGCAGAAGAATTACCTCCTGTTTTGGTGGGTCTCCTGGAAAAATCTCAGG
TGAACGTTTTTCACTGTGGATGCGTCATCGCAGAAATACGGGACTACAGGCAGTCCAGTGACGTGGAGGCCCCTGGTTAC
CAGAGCAGGTGCATTCTCTTACGACCAACCATGCAGACGTTAGCCTGCGACGTAGAGTCCCTAACCAGCGACAGCCAGAC
ATGGACCCAGGAGGACAAACTGTTGCTCGAGAGCCAGCTGATCTTAGCCACAGCTGAACCACTGTGTCTTGATCCTTCTG
TGTCAGTAGCCTGCACTGCAAACAGTCTGCTTTATAACAAACAAAAGATGAACACTGACCCAATGAAGCGCTGCTTCAAG
AGGTGCTCGAGCCCGGCTCTGAGTCGGCAGCAGGAGCTGTCTCATGGCCCACCTCCGCCCGAGCTAACGGTACTGACTTC
TTGCCAACCAAGCAAAGAGAGTAACGCAGGTGAGCAGTATGACCTCAAAATTTCTGGAGCAGGGAATTATGTGGATGTGT
GGGAACAGAGACCCTGTGACTTGGCCGTACCTTCTGAAGTGGATGTGGAGAAATATGCTACAGGGAAGAAGTCCGTGAGC
TCTGATGACTCCCAGCCAACAGGCTGGCCAGCCCATGAAGTCAGAGATGATTCTGTATTTGAATGGGAAGCAGGCGATCA
GTACCGGGATACAAAGATGTTCTTCATGCGCTCGCTTAATGATCCACTTATCTCTGGGAAAGAAATGTCACCTAAAAAAG
CCAGATATGAGAGACAGCTGTCTCCCCCCCACCCCTCCAGAGGTGACCATTCAAAGAGTTTCATGCCTGGGTCGAAGACT
GATGCTGGGACGGTAGTCATTCGGCCCGAGGAATTGGTCCAGAAGAACAGCAGTTGTCCAGTCAAGGTGTCACACAGCTC
CAGTGGCTCAGCCAGTCTCAGCCCACTTTCTCCAGGGAAGGAAACAGAACGGCCTAAGACCGTGCTGCTTCAGGCCTCAG
TCCTGGGGGAGGAAGTCCAACCTCCACCGCCGCCCGTCACGCTGCCCTCGAGCTCAGGCACGAGTTCCTCAGCCAGCAGT
TTTCCTCCACAGCAGGCAGGCGGCTTTCCTAAGTCTGCATCTCCTGCTCCTGCTTCTAAGCCACCAAGTCTTCCCCAGAA
CTCCCCTGTGGAAGTGAGTCGAGTTAGCACGCTTCCTGCAGCCGCCCAGTCCACTGCTGGCTCATCACAAACACAGGTGA
TCACCCAGGTCAGGGTCAGCCCCGTTGGTGTCAGGGTCATCAAAGTGGTGAATTCTGTTCCCGGAACCCACGCTTTGGTG
AGAGCTCCCAACCCCTCGCAGGGCTCTGCCACTGGGGCCACAGCTCCCACGGGAATCTTGCCCAGCAACCTGCCCTTAAG
AGGCCAGCCACCAAAAGCGCCACCCACTGCCCTGCAAGCGAATTCTCAAGTAGGTGTTCGAGTGATTTTAAAAGATGCTC
CAGGTGCCAGGCCCTTAACTCTGCTCCAGTTTCCACCAGGTTCGCTCATTGTGAACACCCAGCAGCTGCCTGGGCAGCTG
CAGCAGCAGCACCTCTATCAGCTGATTCCAGAGCTACAGGGTCAGCAGCCCTCCACTTCGCATCCTCAGCAGCTAGTGTC
ACAGGGTGCAAGTGCACAAGGTTCAGCCAGTCAGAAAACGGCCTTCTGTGCCCAGCAAGCTGTTGTTGTTAACGTCAGTA
GAAGTTTTCTGCAGCCCCAGGTGATTGTGTTGTCTCCGCCTGTCCCTGCCCCGCAAAGACCTGGGCAAAGCCTTCCTCTG
CAGAGAGTCCAGCTCTCCTCCGCC

Alignment

ORF - retro_ecab_1052 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.52 %
• Parental protein coverage: 93.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQQALELALDRAEYVIESARQRPPKRKYLSSGRKSVFQKLYDLYIEECEKEPEV-KKLRRNVNLLEKLVM
          MQ.ALE.ALDRA..VIESA.QRPPKRKY.S.G.KSV..KLYD.Y.EEC..EPEV...LR.NVNLLEKLV.
Retrocopy MQHALERALDRAACVIESAQQRPPKRKYASRGEKSVYEKLYDIYVEECDREPEVAEELRSNVNLLEKLVQ

Parental  QETLSCLVVNLYPGNEGYSLMLRGKNGSDSETIRLPYEEGELLEYLDAEELPPILVDLLEKSQVNIFHCG
          .E.LS.LVVNL.PG..GYSLMLRG.NGS.SETIRL.YEEGELL.YLDAEELPP.LV.LLEKSQVN.FHCG
Retrocopy RESLSRLVVNLHPGGQGYSLMLRGENGSYSETIRLSYEEGELLQYLDAEELPPVLVGLLEKSQVNVFHCG

Parental  CVIAEIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSITSDNHKWTQEDKLLLESQLILATAEPLCL
          CVIAEIRDYRQSS....PGYQSR.ILLRPTMQTL.CDV.S.TSD...WTQEDKLLLESQLILATAEPLCL
Retrocopy CVIAEIRDYRQSSDVEAPGYQSRCILLRPTMQTLACDVESLTSDSQTWTQEDKLLLESQLILATAEPLCL

Parental  DPSIAVTCTANRLLYNKQKMNTRPMKRCFKRYSRSSLNRQQDLSHCPPPPQLKLLDFLQKRKERKAGQHY
          DPS..V.CTAN.LLYNKQKMNT.PMKRCFKR.S...L.RQQ.LSH.PPPP.L..L...Q..KE..AG..Y
Retrocopy DPSVSVACTANSLLYNKQKMNTDPMKRCFKRCSSPALSRQQELSHGPPPPELTVLTSCQPSKESNAGEQY

Parental  DLKISKAGNCVDMWKQSPCNLAIPSEVDVEKYAKVEKSIKSDDSQPTVWPAHDVKDDYVFECEAGNQYQK
          DLKIS.AGN.VD.W.Q.PC.LA.PSEVDVEKYA...KS..SDDSQPT.WPAH.V.DD.VFE.EAG.QY..
Retrocopy DLKISGAGNYVDVWEQRPCDLAVPSEVDVEKYATGKKSVSSDDSQPTGWPAHEVRDDSVFEWEAGDQYRD

Parental  TKLTILQSLGDPLYYGRIQPCKEDEESDSQMSPSHSSTDDHSNWFIIGSKTDAERVVNQYQELVQNEAKC
          TK.....SL.DPL..G.....K.......Q.SP.H.S..DHS..F..GSKTDA..VV....ELVQ....C
Retrocopy TKMFFMRSLNDPLISGKEMSPKK-ARYERQLSPPHPSRGDHSKSFMPGSKTDAGTVVIRPEELVQKNSSC

Parental  PVKMSHSSSGSASLSQLSPGKDTEQPETVSVQSSVLGKGVKHRPPPIKLPSSSGNSSSGNYFTPQQTSSF
          PVK.SHSSSGSASLS.LSPGK.TE.P.TV..Q.SVLG..V...PPP..LPSSSG.SSS...F.PQQ...F
Retrocopy PVKVSHSSSGSASLSPLSPGKETERPKTVLLQASVLGEEVQPPPPPVTLPSSSGTSSSASSFPPQQAGGF

Parental  LKSPTPPPASKPPSLSRKSSVDLNQVSMLSPAALSPASSSQRTTATQVMANSAGLNFINVVGSVCGAQAL
          .KS..P.PASKPPSL...S.V....VS.L..AA.S.A.SSQ....TQV.....G...I.VV.SV.G..AL
Retrocopy PKSASPAPASKPPSLPQNSPVEVSRVSTLPAAAQSTAGSSQTQVITQVRVSPVGVRVIKVVNSVPGTHAL

Parental  MSGSNPMLGCNTGAITPAGINLSGLLPSGSLLPNALPGAMQATSQAGVPFGLKNTSSLRPLNLLQLPGGS
          ....NP..G..TGA..P.GI.L...LP.....P.A.P.A.QA.SQ.GV...LK.....RPL.LLQ.P.GS
Retrocopy VRAPNPSQGSATGATAPTGI-LPSNLPLRGQPPKAPPTALQANSQVGVRVILKDAPGARPLTLLQFPPGS

Parental  LIFNTLQ---QQQQQ-LSQFTPQ-QPQQPTTSSPQQPGEQG-SEQGSTSQEQALSAQHAAVINLAGVGSF
          LI.NT.Q...Q.QQQ.L.Q..P..Q.QQP.TS.PQQ...QG.S.QGS.SQ..A..AQ.A.V.N.....SF
Retrocopy LIVNTQQLPGQLQQQHLYQLIPELQGQQPSTSHPQQLVSQGASAQGSASQKTAFCAQQAVVVNVS--RSF

Parental  MQSQAAVLSQLGSAENRPEQSLPQQRFQLSSA
          .Q.Q..VLS....A..RP.QSLP.QR.QLSSA
Retrocopy LQPQVIVLSPPVPAPQRPGQSLPLQRVQLSSA

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	5.96 RPM
SRP021940_cerebellum	0.00 RPM	17.86 RPM
SRP021940_embryo	0.00 RPM	33.81 RPM
SRP021940_placental_villous	0.00 RPM	15.20 RPM
SRP021940_synovial_membrane	0.00 RPM	10.76 RPM
SRP021940_testis	0.26 RPM	93.10 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1052 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1052 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1052 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4659
Pan troglodytes	retro_ptro_3095
Pongo abelii	retro_pabe_3619
Macaca mulatta	retro_mmul_2479

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000116	2 retrocopies	retro_ecab_1052 , retro_ecab_1101,
Homo sapiens	ENSG00000102710	2 retrocopies	retro_hsap_4659, retro_hsap_4794,
Loxodonta africana	ENSLAFG00000027507	1 retrocopy	retro_lafr_1199,
Macaca mulatta	ENSMMUG00000003590	2 retrocopies	retro_mmul_2479, retro_mmul_2555,
Pongo abelii	ENSPPYG00000005288	2 retrocopies	retro_pabe_3619, retro_pabe_3729,
Pan troglodytes	ENSPTRG00000005791	2 retrocopies	retro_ptro_3095, retro_ptro_3189,
Pteropus vampyrus	ENSPVAG00000014609	1 retrocopy	retro_pvam_401,
Tarsius syrichta	ENSTSYG00000013227	1 retrocopy	retro_tsyr_2160,
Vicugna pacos	ENSVPAG00000007288	1 retrocopy	retro_vpac_193,