RetrogeneDB ID: retro_ecab_492

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:64202769..64203598(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: G6PD
• Ensembl ID: ENSECAG00000014994
• Aliases: None
• Description: glucose-6-phosphate dehydrogenase [Source:HGNC Symbol;Acc:4057]

Sequence

>retro_ecab_492
AGTGAGCCCTTCTTCAGGGCCATCCCGGAGAAGCCCAAACTGGAGGAGTTCTTTGCCTGAAACTCGGGTGTAGCTGGCAT
GTAGGAGGACGTGGCCTCCTACGAGTGTCTTAACAGCCACATGAACACCCTTCACCAAGGGCCAAAAGCCAACTACCTCT
TAAACCTGGCTTTGCCTTCAACCATCTATGAGGCTGTCACTAAGAACATCTGCAAGAACCGCATGATCCAGACAGACTGG
AACCACATCACCATGGAGTAGCCCTTTGGGAAGGACTGGTAGCACCCCATCAGCTGTCTACCCACATCTCCTCCATATTC
CACAAGGACCAGATCTATTGCATCAGCCACTACTTAGGCAAGGAGATGGTCCAGAACCTCATGGTGCTGAGGTTTGCCAA
CAGGATCTTTGGCCCCATCTGGAGCCAGAACAATGTCACTTGCGTCATCCTTATTGTCAAGGAGCCCTTTGGCGCTGAGG
GCCATGGGGGGCTACCTTGATGAATTTGAGACATCCTAGACATGATGCAGAACCACCTCACACAGGTGCTATGTCTGGTG
GCCATGGAGAAGCTCGCCTCCATGGACTCAGATGACGCACATTACTAGAAGGTCAAAGTGTTCAAACGTTATCTCAAAAG
TGCAGGTTAACAACATTGTCCTGGGTCAGTATGTGGGGAACACCAACGAGAGGGCGAGGCCACCAAAGGGTACCTGGCTG
TCCCCACAGTGACCCACGGGTCCGCAACTGCCACCTTCACTGCTGTCGTCCTCTATGTAGAGAATGAGAGGTGGGACAGG
CGTCCTTCATCCTGTGCTTTGGCAAGGCT

Alignment

ORF - retro_ecab_492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.66 %
• Parental protein coverage: 53.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SEPFFKATPEEKPKLEEFFARNSYVAGQYDDSASYKRLNSHMNALHQGSQANRLFYLALPPSVYEAVTKN
          SEPFF.A.PE.KPKLEEFFA.NS.VAG...D.ASY..LNSHMN.LHQG..AN.L..LALP...YEAVTKN
Retrocopy SEPFFRAIPE-KPKLEEFFA*NSGVAGM*EDVASYECLNSHMNTLHQGPKANYLLNLALPSTIYEAVTKN

Parental  IHETCMSQTGWNRIIVEKPFGRD-LQSSDQLSNHISSLFREDQIYRIDHYLGKEMVQNLMVLRFANRIFG
          I....M.QT.WN.I..E.PFG.D.L....QLS.HISS.F..DQIY.I.HYLGKEMVQNLMVLRFANRIFG
Retrocopy ICKNRMIQTDWNHITME*PFGKD<LVAPHQLSTHISSIFHKDQIYCISHYLGKEMVQNLMVLRFANRIFG

Parental  PIWNRDNIACVILTFKEPFGTEGR-GGYFDEFGI-IRDVMQNHLLQMLCLVAMEKPASTDSDDVRDEKVK
          PIW...N..CVIL..KEPFG.EG..GGY.DEF...I.D.MQNHL.Q.LCLVAMEK.AS.DSDD....KVK
Retrocopy PIWSQNNVTCVILIVKEPFGAEGH>GGYLDEFET<ILDMMQNHLTQVLCLVAMEKLASMDSDDAHY*KVK

Parental  VLK-CISEVQADHVVLGQYVGNPS-GEGEATKGYLDDPTVPRGSTTATFAAVVLYVENERWDGVP-FILR
          V.K..IS.VQ....VLGQYVGN....EGEATKGYL..PTV..GS.TATF.AVVLYVENERWD..P.FIL.
Retrocopy VFK>VISKVQVNNIVLGQYVGNTN<REGEATKGYLAVPTVTHGSATATFTAVVLYVENERWDRRP<FILC

Parental  CGKA
          .GKA
Retrocopy FGKA

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	16.88 RPM
SRP021940_cerebellum	0.05 RPM	69.02 RPM
SRP021940_embryo	0.00 RPM	81.83 RPM
SRP021940_placental_villous	0.00 RPM	73.32 RPM
SRP021940_synovial_membrane	0.00 RPM	92.79 RPM
SRP021940_testis	0.00 RPM	55.18 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_492 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_492 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
Callithrix jacchus	ENSCJAG00000016775	2 retrocopies	retro_cjac_4026, retro_cjac_499,
Equus caballus	ENSECAG00000014994	1 retrocopy	retro_ecab_492 ,
Myotis lucifugus	ENSMLUG00000008210	1 retrocopy	retro_mluc_842,
Mus musculus	ENSMUSG00000031400	1 retrocopy	retro_mmus_174,
Sus scrofa	ENSSSCG00000025108	1 retrocopy	retro_sscr_818,