RetrogeneDB ID: retro_ecab_349

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:40070246..40070629(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA0947
• Ensembl ID: ENSECAG00000023968
• Aliases: None
• Description: KIAA0947 [Source:HGNC Symbol;Acc:29154]

Sequence

>retro_ecab_349
CAAGGATGTCCAGAAACAGAATTTCACACCAGTGAAAAACTTGGTGATCTAAGTGATAACACTTGGGAACACATAATTGC
CATCTGTCTTCTCTGCTGCCATGAGCAATAGATTTGCACACATGATAAGATCATAAGTAAAGAGCTGTGGCTTGTAATGG
ATAAGTGGATAAAATGCAGAAAAGGACTTGTGAGCATTGCATATACTCCTGATATTATTATGGCATCAATACTGAGGCTG
ATGGTCATTTAGGCCCATTGGATTTGAAGAAATGGTTTCCATCTCATGTCAAAAATATCAGTTTGGTTATGGATATGTTT
ATACAGCATGTTCAAGATGAAGATATACCATGGGGTACACAGTTAGCAGCTGTGTGTACACTC

Alignment

ORF - retro_ecab_349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 55.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLCPNTEFQSSERFGEDLSENTWEYVLAIDLLCCHQKWVWTHDHIISKELWPVMDKWIKYRKGHANIAHT
          Q.CP.TEF..SE..G.DLS.NTWE...AI.LLCCH.....THD.IISKELW.VMDKWIK.RKG...IA.T
Retrocopy QGCPETEFHTSEKLG-DLSDNTWEHIIAICLLCCHEQ*ICTHDKIISKELWLVMDKWIKCRKGLVSIAYT

Parental  PDVIIASVLRLI-GRLGQLGLKEGFPSAVKNISSVIGMFIQHAQDEDIPWGIQLAAVYAL
          PD.I.AS.LRL..G.LG.L.LK..FPS.VKNIS.V..MFIQH.QDEDIPWG.QLAAV..L
Retrocopy PDIIMASILRLM<GHLGPLDLKKWFPSHVKNISLVMDMFIQHVQDEDIPWGTQLAAVCTL

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	12.57 RPM
SRP021940_cerebellum	0.00 RPM	14.28 RPM
SRP021940_embryo	0.00 RPM	61.48 RPM
SRP021940_placental_villous	0.00 RPM	25.93 RPM
SRP021940_synovial_membrane	0.00 RPM	23.80 RPM
SRP021940_testis	0.00 RPM	14.26 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_349 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_349 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_349 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023968	1 retrocopy	retro_ecab_349 ,