RetrogeneDB ID: retro_pcap_19

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_36188:16406..17855(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000016788
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSPCAG00000014683
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_pcap_19
ATGGCAGAGACTGCAGCTCCCTCAGAAGCCTACGAGGCCTCCGGTGCCGAGGCAAGTGCCGGGGCGGCTGAGGAAAGTGG
CCGGAAACCCGGCCTGCCGGCGCCCGAGGCATCCCGGGAGCTGGCAGCGCGAAGCCCCGCCCCGACTCGAGCGTCAGGCT
TAAGGCCCGCCCAGGGCGCAGGGGGAGGGGCCAGGCCATTACCCTTGCCGGGCCGAAGCAGCGGCAGCTGGACAAAGTTG
GTGACCTGCAGGTATTATCTACATGGGCTGTGCAAGGAAGGGGAGAACTGCCGTTATTCTCATGACCTCTCAGGCCGGCC
GCCAGCTACCGTGGGCCCCGATGCGGCCCTCCGCGCCTATGCCGATAGCCGCGGTGACGCGGCTGCGCAAATCAGGGCCC
GGGCTCCGGAAGTGGCGGGAACTTCCCGTGGTACTTCCTCTCTCTCCTTGCCTCTGATTGGCTCGGCTGCTGAAGGGCGT
TTCTTTGGAGAGGAGGCCGACAATGGCGGCGGTGTAGCCGCCGGCGCGAGCTCGGCATCTTGGGCGGATGCTGTTGAGTT
TGTTCCGGGGCAGCCTTACCGAGGACGCTGGGCACTGTATGCTCCGGAGACTTCACCGCAGAGCTCGTTAACAGAAACGG
AGCACAGCGCTGTTGGCGCGGGCGAGCCGCTTTGCCCTTACGCAGCTGTAGGAGAATGCCCTGATGGGGAGAGGTGTGTG
TACCTCCACGGAGAGGCTTGCGACATGTGTGGGCTGCAGATACTGCATCCCGTGGATGCTGCCCAGAGAGCAGAGCACAT
AAAGTCTTGCATAGAAGCTCACGAGAGGGATATGGAGCTCTCTTTCGCTGTGCAGTGCAGTATGGACAAAGTGTGTGGCA
TCTGCATGGAGGTGGTTTATGAGAAAGCCAACCCCAACGATCGCCGCTTTGGCGTCTTGTCTAACTGCAACCACACCTAC
TGTCTTAAGTGTATCCGTGAGTGGAGGAGAGCCAGACAGTTTGAAAACAGGGTTGTCAAATCGTGCCCACAGTGCAGGGT
CCCCTCAGACCTTGTCATTCCCAGTGAATTCTGGGTGGAGGAAGAGGAAAAGAAACAGACGCTTATTCAGCAGTACAAGG
AAGCAATGAGCAACAAGCCCTGCAGGTATTTTGCTGAAGGTAGAGGTCACTGCCGCTTTGGAGAGCACTGTTTTTACAAG
CATGCTTACCCTGAAAGTCAGGAACCACCTCAAAGGCAAGATGCTGGAACATTCAGCACTTACTGGAGTAAGTTTGTAGA
GGTCAGCATGCCCTTTAAGGGCCATGAAAAGGGTCTTGTCAGGCTTCATCTGTCCAAGCTATTGTTTAGGCGTCTTCTTT
TGAAAGGGTATGAAAAATTCCCCTTCTCTGAGGACCTGTGGGAATTGCTTCTTTTTGAGCTTGAAAAATATTTAAATTTG
ATTCTGTAG

Alignment

ORF - retro_pcap_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.8 %
• Parental protein coverage: 60.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSVGAGADDWANAVEFVPGQPYCGRTAPSCTEAPPQGSVTKEESEEDQPSMETKKQLCPYAAVGECRYGE
          V..GA....WA.AVEFVPGQPY.GR.A....E..PQ.S.T....E...........LCPYAAVGEC..GE
Retrocopy VAAGASSASWADAVEFVPGQPYRGRWALYAPETSPQSSLT----ETEHSAVGAGEPLCPYAAVGECPDGE

Parental  NCVYLHGDSCDMCGLQVLHPVDAAQRSQHIRSCIEAHEKDMELSFAVQRSKDVVCGICMEVVYEKANPGE
          .CVYLHG..CDMCGLQ.LHPVDAAQR..HI.SCIEAHE.DMELSFAVQ.S.D.VCGICMEVVYEKANP..
Retrocopy RCVYLHGEACDMCGLQILHPVDAAQRAEHIKSCIEAHERDMELSFAVQCSMDKVCGICMEVVYEKANPND

Parental  RRFGILSSCSHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPCEYWVEEKEEKQRLVQKYKEAMS
          RRFG.LS.C.HTYCLKCIR.WR.A.QFE....KSCP.CR..S..VIP.E.WVEE.E.KQ.L.Q.YKEAMS
Retrocopy RRFGVLSNCNHTYCLKCIREWRRARQFENRVVKSCPQCRVPSDLVIPSEFWVEEEEKKQTLIQQYKEAMS

Parental  NKACRYFDEGRGSCPFGGNCFYKHAYPDGRTEEPQRQKVGASS
          NK.CRYF.EGRG.C.FG..CFYKHAYP....E.PQRQ..G..S
Retrocopy NKPCRYFAEGRGHCRFGEHCFYKHAYPESQ-EPPQRQDAGTFS

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_19 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Ochotona princeps	ENSOPRG00000010353	1 retrocopy	retro_opri_1073,
Procavia capensis	ENSPCAG00000014683	1 retrocopy	retro_pcap_19 ,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Tupaia belangeri	ENSTBEG00000004564	2 retrocopies	retro_tbel_1410, retro_tbel_71,