RetrogeneDB ID: retro_ecab_846

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:91932916..91933704(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGOL1
• Ensembl ID: ENSECAG00000012475
• Aliases: None
• Description: shugoshin-like 1 (S. pombe) [Source:HGNC Symbol;Acc:25088]

Sequence

>retro_ecab_846
CAAATAATCACCAACATTTCTATGTACTTGAAAAATTACCCTGAGTACAATAGAATGTCAGTGTTAGATGTAGAAAAATT
CAAAGTGAGAGAAGCCTAAGACACCATCCTACAACTGAGAAAGGAATTTTACTACCTTGAATGTCAGCTATTTGCTTTGA
AAGAAAAATGCACTTCAGAACAAAGAGAAAAACCCTTCAAAACCAGTAAGTACTTCCCTTTTGAATGGACTCCAATAATA
ATGATGATTCCAAGGACTTATTAGTGAAGGGTTTACCTCAAGCTCCTCTCAGAAAGTTGCCCTTCCAGAACAAAGAGAAT
CATTACAAATAGAAGAGCAATATCTGCTATTCCTCAAGACAGATTCGATTCGGCATATTCTAGTTCAGGTGAACATAATC
TACTGACGTCTTTCACGGAACTCTCTCTCTCCATCCGCCGCAGTTTAGGGAAAAGCTTTAACGATCTTGGGAAATTCGAT
AACTTGGATGACTTTGAAATGAGTCATCTGTCAGGGAAGTCTTTTGACCTGGAAAGAATTAAATCTGCAAACCCTCTAGG
AGGTATACACATACTGAAAATGTAGAACAAAATGTTTGTCGATGGAGCAAGGACAAAATTAACTTATTACCAAGGCTAAT
TTACCTAGAAAGAATTACTAACACGGAAGAAGTCATTTTCAGCAAAAATTTGAACAAACTAAAACTAAGCTTACAGACTC
ACAATGAAGAAAAAGATAAAAGAAAAGCTAACAGAAGGAGAAAATCAAAATGCGTTTCAAGATACAAA

Alignment

ORF - retro_ecab_846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.88 %
• Parental protein coverage: 50.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  QIITNTSTLLKNYQDNNRMLVLALENEKSKVREAEDIILQLRKECYYLTCQLYTLKEKLTSQEAEG-TAQ
          QIITN.S..LKNY...NRM.VL..E..K.KVREA.D.ILQLRKE.YYL.CQL..LKEK.TS...E..T.Q
Retrocopy QIITNISMYLKNYPEYNRMSVLDVE--KFKVREA*DTILQLRKEFYYLECQLFALKEKCTSEQREK<TLQ

Parental  NQEVCLSEMDSNG-DNSRDLFVTDLPQVPL-QEAHLPGPGESFQIEEQ-IPTIPNQDRQRFDLDSGEDKS
          NQ.V....MDSN..D.S.DL.V..LPQ.PL.Q...LP...ES.QIEEQ.I..IP..........SGE...
Retrocopy NQ*VLPF*MDSNNNDDSKDLLVKGLPQAPL<QKVALPEQRESLQIEEQ<ISAIPQDRFDSAYSSSGEHNL

Parental  TDNVLPRTVSLRRSLKKRFNNLCQFDTLDDFEISHLSGQSFELERIRFVDPLISVHI-PENVEENVCQWN
          .........S.RRSL.K.FN.L..FD.LDDFE.SHLSG.SF.LERI....PL...HI..ENVE.NVC.W.
Retrocopy LTSFTELSLSIRRSLGKSFNDLGKFDNLDDFEMSHLSGKSFDLERIKSANPLGGIHI<TENVEQNVCRWS

Parental  KDQINLSPKLIHPGKSTKTNEDIL-EYKSEPTKRKHRDAHGRK-EKRKANRRRKSKCISKYK
          KD.INL.P.LI.....T.T.E.I....K.E.TK.K..D...RK..KRKANRRRKSKC.S.YK
Retrocopy KDKINLLPRLIYLERITNTEEVIF<QQKFEQTKTKLTDSQ*RK>DKRKANRRRKSKCVSRYK

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	0.18 RPM
SRP021940_cerebellum	0.00 RPM	0.10 RPM
SRP021940_embryo	0.00 RPM	9.90 RPM
SRP021940_placental_villous	0.00 RPM	0.19 RPM
SRP021940_synovial_membrane	0.00 RPM	0.44 RPM
SRP021940_testis	0.00 RPM	3.52 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_846 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_846 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_846 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013948	1 retrocopy	retro_chof_2699,
Dasypus novemcinctus	ENSDNOG00000008694	1 retrocopy	retro_dnov_1045,
Equus caballus	ENSECAG00000012475	1 retrocopy	retro_ecab_846 ,
Mus musculus	ENSMUSG00000023940	2 retrocopies	retro_mmus_3486, retro_mmus_867,
Rattus norvegicus	ENSRNOG00000022499	1 retrocopy	retro_rnor_2440,