RetrogeneDB ID: retro_pcap_444

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_89485:9849..10399(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf40
• Ensembl ID: ENSPCAG00000009727
• Aliases: None
• Description: chromosome 19 open reading frame 40 [Source:HGNC Symbol;Acc:28467]

Sequence

>retro_pcap_444
CCTGATGACACAGGCCTCATACCCGTGCCTTTAGCATACACTGTGCCCAGTAAGAAACAGCATGGGTTGTAGGTGGTGCA
TGGATCTAAGAGAAAATTAAACTCAGTTTTGAGGATTACCTGATGCCAGCAGATTTTCATTTGTGTAAGATATCCTGTAG
TCTTTGTATCACTCAAGCTGATTTGGTGACATGAAATGGCTGCAGAAAGAGGCTTGTTCCAATAAGAAACTGCAGTTACC
TTCAAGGGGCTATACTAGTTGAAAAGATACATATTGGTGAACAATATTTTTCAGATGTACTGAAGTTTACTGTGCTGGGT
CTTGCGATGGTGTTGCTTTCAGTAACTGGCCTGGCAGATGGAAGCGTCTAACTCATTATATAGTTAGTCCAAGAACAAAC
CAAAGAGCCCAATAAGAACACTTTTTCTCAGGAAGCCCCATGGTCTGCTCTCTGAACCATCCCTCCTTTGAACTGTGTTA
GCAGATCACCGGAACTGGAAAAGTTGCGGCGCCCTTTCTGCTTCAGAAATTCTCAAGTGCCCGACAACTA

Alignment

ORF - retro_pcap_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.91 %
• Parental protein coverage: 84.65 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PDDTEPIHVPFGYVVASEKWRGSQLVQGMQGK-IKLLFEDRLTAVDFYLSNRSCVLYITEADLVAGNGYR
          PDDT..I.VP..Y.V.S.K..G...V.G...K.IKL.FED.L...DF.L...SC.L.IT.ADLV..NG.R
Retrocopy PDDTGLIPVPLAYTVPSKKQHGL*VVHGSKRK<IKLSFEDYLMPADFHLCKISCSLCITQADLVT*NGCR

Parental  KRLVRVRNPGNLQGIVIFEKTQMSEQYFAAVQKFTVLDLGMVLLPVASQAEASS-LIIQLVQEQIKELAK
          KRLV..RN...LQG....EK....EQYF..V.KFTVL.L.MVLL.V...A..S..LII.LVQEQ.KE..K
Retrocopy KRLVPIRNCSYLQGAILVEKIHIGEQYFSDVLKFTVLGLAMVLLSVTGLADGSV*LII*LVQEQTKEPNK

Parental  NP-FVRKKCAVLAEPALLRTVQ-QIPGVGKVKAPLLLQKFPSIQQL
          N..F.RK....L.EP.LL.TV..QI.G.GKV.AP.LLQKF.S..QL
Retrocopy NT>FLRKPHGLLSEPSLL*TVL>QITGTGKVAAPFLLQKFSSARQL

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_444 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000728	2 retrocopies	retro_cjac_1011, retro_cjac_3952,
Cavia porcellus	ENSCPOG00000011965	1 retrocopy	retro_cpor_1536,
Dasypus novemcinctus	ENSDNOG00000014134	4 retrocopies	retro_dnov_1817, retro_dnov_2382, retro_dnov_426, retro_dnov_942,
Echinops telfairi	ENSETEG00000002716	1 retrocopy	retro_etel_458,
Loxodonta africana	ENSLAFG00000006401	4 retrocopies	retro_lafr_165, retro_lafr_365, retro_lafr_415, retro_lafr_789,
Myotis lucifugus	ENSMLUG00000013287	1 retrocopy	retro_mluc_522,
Macaca mulatta	ENSMMUG00000017939	1 retrocopy	retro_mmul_788,
Procavia capensis	ENSPCAG00000009727	1 retrocopy	retro_pcap_444 ,
Sarcophilus harrisii	ENSSHAG00000016372	1 retrocopy	retro_shar_299,