RetrogeneDB ID: retro_pcap_403

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_69794:854..1300(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CETN3
• Ensembl ID: ENSPCAG00000006854
• Aliases: None
• Description: centrin, EF-hand protein, 3 [Source:HGNC Symbol;Acc:1868]

Sequence

>retro_pcap_403
ATGAGTTTATCTCTGAGAAACAAGTATTTAGTGGACAAAACAAAGAGAAAGTATCAAAGAGAACTCTCTGAAGAACAGAA
GCAAGAAATTCAAGATGCTTTTTAACTATCTGATACAGACAAAGATGAATCAATAGATTATCATGAATTAAAGGTGAAAA
CGAGAATTTTGGAGTTTGATGTAAAAAAACCTGATGTAACAAAGATTCTTAAAAGATATGACCAGGAAGCCACTGGAAAA
ATCATCTTTGAAGATTTTCATGAGGTTATAACAGATTGGATGTTAGACAGAGACCTGCATGAAGAAATCTTGAAGGGATT
AAACTATTTGACAAGGATGATTCAGGTAAAATAAGCTTGAAGAATTCATGACATGTTGCCTGAGAATTAGGTGAAAGGAT
GAATGATGAAGAACTTTGAGCTATAATAGAAGAATTTGATAAAGAT

Alignment

ORF - retro_pcap_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.33 %
• Parental protein coverage: 89.22 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLALRNDLLVDKTKRKKRRELSEEQKQEIKDAFELFDTDKDEAIDYHELKVAMRALGFDVKKADVLKIL
          MSL.LRN..LVDKTKRK..RELSEEQKQEI.DAF.L.DTDKDE.IDYHELKV..R.L.FDVKK.DV.KIL
Retrocopy MSLSLRNKYLVDKTKRKYQRELSEEQKQEIQDAF*LSDTDKDESIDYHELKVKTRILEFDVKKPDVTKIL

Parental  KDYDREATGKITFDDFNEVVTDWILERDPHEEILK-AFKLFDDDDSGKISLRNLRRVARELGENMSDEEL
          K.YD.EATGKI.F.DF.EV.TDW.L.RD.HEEILK...KLFD.DDSGKISL.N...VA.ELGE.M.DEEL
Retrocopy KRYDQEATGKIIFEDFHEVITDWMLDRDLHEEILK<GIKLFDKDDSGKISLKNS*HVA*ELGERMNDEEL

Parental  RAMIEEFDKD
          .A.IEEFDKD
Retrocopy *AIIEEFDKD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_403 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007233	1 retrocopy	retro_dord_30,
Otolemur garnettii	ENSOGAG00000002383	1 retrocopy	retro_ogar_3511,
Ochotona princeps	ENSOPRG00000002381	1 retrocopy	retro_opri_17,
Procavia capensis	ENSPCAG00000003203	1 retrocopy	retro_pcap_149,
Procavia capensis	ENSPCAG00000006854	1 retrocopy	retro_pcap_403 ,
Procavia capensis	ENSPCAG00000007778	1 retrocopy	retro_pcap_364,
Pteropus vampyrus	ENSPVAG00000017925	1 retrocopy	retro_pvam_19,
Tupaia belangeri	ENSTBEG00000001992	2 retrocopies	retro_tbel_4470, retro_tbel_4732,