RetrogeneDB ID: retro_pcap_71

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_3917:23843..24854(+)
• Located in intron of: ENSPCAG00000011081

Retrocopy information

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

Parental gene information

• Parental gene symbol: ECI2
• Ensembl ID: ENSPCAG00000008568
• Aliases: None
• Description: enoyl-CoA delta isomerase 2 [Source:HGNC Symbol;Acc:14601]

Sequence

>retro_pcap_71
GAATCCAGTCTTCTGCAGGTGCATAGCTTCTCGGTGCTTCGGATACACACGAGCCAAACAGCAATGACAGCCAGTCAGAA
GGACTTTGAGACAGCAGTGAATCAGATGAAGCTCTTGAGCAAAGACCCAGGAAATGAAATAAAACTAAAACTGTACTCCT
TGTATAAACAGGCCACTGAAGGACCTTGTAATACGCCCAAACCAGGTATGCTTGACTTCGTCAACAAGGCCAAATGGGAT
GCATGGAGTGCCCTTGGTAGCCTGCCCAAGAAAACCGCCAAGCAGAACTATGTGGAGCTGGTGTCAAGTTTGAGTTCATC
TAAATCCCCTAGCCACGGGAAGCCTGTGGCAGACGGTCAGCAGCCTGCACACAGAGACCTAGTGGTGACCTCAGAAGATG
GCATCACCAAGATCGTGTTCAACCGTCCCACCAGAAAAAATGCCATCACCACTGAGATGTATGAGGAAATTATGTGTGCA
CTTGAAGCGGCAGGGAAGGATGACTCAGCCATAACTGTGTTAACAGGAAATGGTGATTATTATTGTAGCAGGAATGATCT
GAACAACTTCACTGACATTCCCCCTGGTGGCGTAGAAGAGCAAGCCAAAAACAGTGCCATCTTGCTAAGAAATTTTGTAG
GCTGCTTTATAGATTTCCCCAAGCCTCTAATTGCAGTGGTAAATCGCCCAGCTGTGGGAATCGCCGTCACCCTTCTTGGG
CTGTTTGATGTCGTGTATGCTACTGACAGGGCAACATTTCACACTCCTTTCAGTCACCTAGGCCAGAGTCCAGAAGGCTG
CTCCTCTTACATGTTTCCGAAGATGATGGGCTCAGCCAAGGCAGCTGAGATTCTTCTTTTCGGAAAGAAGTTAACAGCAA
GAGAAGCCTGTGCTCAAGGACTGGCTACTGAGGTTTTTCCCGACAGCACGTTTCAGAAATAAGTTTGGACCAGGCTGAAA
GCCTATTCAAAGCTTCCCCCAAATGCCATGAGAATTTCCAAACAGCTTATC

Alignment

ORF - retro_pcap_71 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.03 %
• Parental protein coverage: 85.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QPGLLQVHSFSVLRIHTSQTAMTASQKDFETAVNQMKLLSKDPGNEIKLKLYSLYKQATEGPCNTPKPGM
          ...LLQVHSFSVLRIHTSQTAMTASQKDFETAVNQMKLLSKDPGNEIKLKLYSLYKQATEGPCNTPKPGM
Retrocopy ESSLLQVHSFSVLRIHTSQTAMTASQKDFETAVNQMKLLSKDPGNEIKLKLYSLYKQATEGPCNTPKPGM

Parental  LDFVNKAKWDAWSALGSLPKETAKQNYVELVSSLSSSESPSHGKPVADGQQPAHRDLVVTSEDGITKIVF
          LDFVNKAKWDAWSALGSLPK.TAKQNYVELVSSLSSS.SPSHGKPVADGQQPAHRDLVVTSEDGITKIVF
Retrocopy LDFVNKAKWDAWSALGSLPKKTAKQNYVELVSSLSSSKSPSHGKPVADGQQPAHRDLVVTSEDGITKIVF

Parental  NRPTRKNAITTEMYEEIMRALEAAGKDDSAITVLTGNGDYYCSGNDLNNFTDIPPGGVEEQAKNSAILLR
          NRPTRKNAITTEMYEEIM.ALEAAGKDDSAITVLTGNGDYYCS.NDLNNFTDIPPGGVEEQAKNSAILLR
Retrocopy NRPTRKNAITTEMYEEIMCALEAAGKDDSAITVLTGNGDYYCSRNDLNNFTDIPPGGVEEQAKNSAILLR

Parental  NFVGCFIDFPKPLIAVVNGPAVGIAVTLLGLFDVVYATDRATFHTPFSHLGQSPEGCSSYMFPKMMGSAK
          NFVGCFIDFPKPLIAVVN.PAVGIAVTLLGLFDVVYATDRATFHTPFSHLGQSPEGCSSYMFPKMMGSAK
Retrocopy NFVGCFIDFPKPLIAVVNRPAVGIAVTLLGLFDVVYATDRATFHTPFSHLGQSPEGCSSYMFPKMMGSAK

Parental  AAEILLFGKKLTAREACAQGLVTEVFPDSTFQKEVWTRLKAYSKLPPNAMRISKQLI
          AAEILLFGKKLTAREACAQGL.TEVFPDSTFQK.VWTRLKAYSKLPPNAMRISKQLI
Retrocopy AAEILLFGKKLTAREACAQGLATEVFPDSTFQK*VWTRLKAYSKLPPNAMRISKQLI

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_71 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009409	1 retrocopy	retro_cfam_536,
Choloepus hoffmanni	ENSCHOG00000009239	1 retrocopy	retro_chof_25,
Procavia capensis	ENSPCAG00000008568	1 retrocopy	retro_pcap_71 ,
Rattus norvegicus	ENSRNOG00000016369	1 retrocopy	retro_rnor_1179,
Tupaia belangeri	ENSTBEG00000015862	2 retrocopies	retro_tbel_2398, retro_tbel_814,