RetrogeneDB ID: retro_pcap_381

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_61028:15298..16135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASB6
• Ensembl ID: ENSPCAG00000013086
• Aliases: None
• Description: ankyrin repeat and SOCS box containing 6 [Source:HGNC Symbol;Acc:17181]

Sequence

>retro_pcap_381
AGCGATGTTCTCCTGCAGAACGGGGTTGGCCTCAACTTCAAAGACCTGGTCACCTACTATACCACCCTGCACAAGGCCTC
TGCATGAAACCAGCCCAGCCCAGTGGAGCTGCCGGCACCCCACTGGGCCGACACTAGTCAGAAGGACCAGATGGACCAGA
GCCGCCCCTCAGCCTGGCAGGAGGAGCCAGAGCACTGCCCTGCTGGCAGCACCTACTATACCTTGGAGCAGATGTCAGTA
TGACTGACAGGCATAGAGATACTGCTCTGCTCCATGCTTGAATCAGCAACGATGGGGTGCAGATCCACAACCCTGAGAAC
ACCCAGCTGTTGCCGGATGGAGGGATGAATGTCAAGGCTACCACCAAAGATCGGGATACTGTGTTCACCTGTCTCGTCTT
TCTGCTCAGTGAAACAGTGGGAGGGGACAGAGAGGAGGCCCACCTGATGAACCTCTTCTGCAGCTAAGTAACACAGCTGC
TGCTGGGGCAGGGGCAGACCCCAGCAAGTGCCCAGGCCACGAAGCCCTCACTCACATCTGCGTCAAGAGCTTTCCACTGC
ATTTCCCTCACCCACACTTCCTGCTGGAGTCCAGAGCCGCCTATAACTGCTCCCTCTACAAGGTGTCCTGCTGCTCTAGT
TTTCTCATCTCTGAGAGGCTCTCTTCGTACCTAGGCTGTACCCAAGATGAGAGTCACATGGACCTTCTGTGTAAAGCGAA
ACCATCCCAGATCTCACGATGACTAACTCCCAGAATCCCCAGCTGCCTCAAAATTTTGACACGTACCCTGGGGGCAGCCT
GGCAGGAAAGATCCAGGCCCTGCACTTCTTGAGGCAG

Alignment

ORF - retro_pcap_381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.19 %
• Parental protein coverage: 73.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ADVLLRNGANLNFEXXXXXXXXXXXXXXXXQPNMVEL-LRHGADINRRDRIHESSPLDLASEEPER-LPC
          .DVLL.NG..LNF.................QP..VEL...H.AD....D....S.P.....EEPE..LPC
Retrocopy SDVLLQNGVGLNFKDLVTYYTTLHKASA*NQPSPVELPAPHWADTSQKDQMDQSRP-SAWQEEPEH<LPC

Parental  LQRLLDLGADVNAADKHGKTALLHALASSDGVQIHNTENIRLLLEGGADVKATTKDGDTVFTCIIFLLSE
          .Q.LL.LGADV...D.H..TALLHA..S.DGVQIHN.EN..LL..GG..VKATTKD.DTVFTC..FLLSE
Retrocopy WQHLLYLGADVSMTDRHRDTALLHA*ISNDGVQIHNPENTQLLPDGGMNVKATTKDRDTVFTCLVFLLSE

Parental  TVGGDKEEAELINRFCFQVTQLLLAH-GADPSECPAHESLTHICLKSFKLHFPLLRLLLESGAAYNCSLH
          TVGGD.EEA.L.N.FC..VTQLLL...GADPS.CP.HE.LTHIC.KSF.LHFP....LLES.AAYNCSL.
Retrocopy TVGGDREEAHLMNLFCS*VTQLLLGQ<GADPSKCPGHEALTHICVKSFPLHFPHPHFLLESRAAYNCSLY

Parental  GASCWSGFHIIFERLCSHPGCAEDESHVDLLHKA-ETVLDLMVTNSQKLQLPENFDIHPVGSLAGKIQAL
          ..SC.S.F..I.ERL.S..GC..DESH.DLL.KA.ET..DL..TNSQ..QLP.NFD..P.GSLAGKIQAL
Retrocopy KVSCCSSF-LISERLSSYLGCTQDESHMDLLCKA<ETIPDLTMTNSQNPQLPQNFDTYPGGSLAGKIQAL

Parental  HFSLRQ
          HF.LRQ
Retrocopy HF-LRQ

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_381 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007753	1 retrocopy	retro_meug_1853,
Procavia capensis	ENSPCAG00000013086	2 retrocopies	retro_pcap_264, retro_pcap_381 ,