RetrogeneDB ID: retro_pcap_462

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_98505:1041..2565(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIM28
• Ensembl ID: ENSPCAG00000007149
• Aliases: None
• Description: tripartite motif containing 28 [Source:HGNC Symbol;Acc:16384]

Sequence

>retro_pcap_462
ACACTGACCTGCCGGGACTGCCAGCTCAATGCCCACAAGGACCATCAATACCAGTTCCTGGAGGATGCAGTGAGGAACCA
GCGCAAACTCCTAGCCTTGTTGGTGAAGCGCCTTGGGGACAAGCATGCCACGCTGCGGAAGAGCACCAAGGAGGTTCGCA
GCTCGATTCGTCATGTGTGAGATGTCCAGAGCATGTGCAGGTGGATGTTAAGATGGCCATCCTGCAGATTATGAAAGAGT
TGAACAAACGGGGCCGCATGCTGGTCAATGATGCCCAGAAAGTGACTGAGAGGCAGCAGAGCGGCTGGAGTGCCAGCACT
GGACCATGACCAAGATCCAGAAGCACAAGGTAACACATCTTGCGTTTTGCCTCCTGGGCCCTGGAAAGTGACAATAACAC
AGCCCTGCTGCTCTCCAAGAAGCTGATCGACTTCCAGCTGCACCGTGCCCTCAAGATGATTGTGGACCCCGTGGAGCCTC
ATGGCGAGATGAAATTCCAGTGGGACCTCAGTGCTTGGACCAAGAGTGCTGAGGCCTTTGGCAAGATCGTGGCAGAGCGC
TGGGGCACCAACTCTACAGGACCTGCACCCATGGCCCCCCCGCGGGTCCCTGGCCCACTGAACAAGCAGGGCTCAGGCAG
CAGTCAACCCATGGAGGTACAGGAAGGCTAACGGCTTTGGGTCAGATGACCCCTACTCGAGTGCGGAGCCTCACGTGTGG
GGTGTGAAGCGATCCTGCTCTGGTGAGGGTGAAGTGAGTGGCCTCATGCGCAAGGTAGCACTTGTGAGTCTTGAGCGCCT
GGACTTGGACCTCACAGCTGACAGCCAGCCACCTATATTGAACGTGTTCCCAGGCAACACCACAGAGGACGGCAATCTCA
TTGTCATTGAACGTGGTGGTGCTGCGGCTGCGGCTGCGGGACAACCAGGAACTGCGCCCCCTGGGGCCCCTGGAGCCCCG
CCCTTGCCTGGCATGGCCATTGTCAAGGAAGAAGAGACAGAGGCAGCCACTGGAGCACCACCTGCAGCTGCAGAAGGCCC
TGAGACCAAGCCTGTGCTTATGGCCCTGGCAGAGGGTCCTGGTGCAGAGGGCTCCCGCTTGGCCTCACCCAGTGGTAGCA
CCAGCTCAGGACTGGAGGTGGTGGCCCCTGAAGGTGCCTCAGCGCCATCAGGTAGTGCAGGCACCCCGGATGACAGTGCC
ACTATTTGTCGCATCTGCCAGCAGCCAGGGGACCTGGTCATGTGCAACCAGTGCGAGTTTTGCTTCCACCTGGACTGTCA
CCTGCCAGCTCTGCAGGATGTGCCAGGGGAAGAGTGGAGCTGTTCACTCTGCCATGTGCTCCCTGACCTGAAAGAGGAGG
ATGGGAGTCTCAATCTGGATGAGGCTGACACCACCAGTGTGGTGGCCAAGCTTTCGCCAGCCAACCAGTGGAAATGTGAG
CGTGTCCTGCTGGCCCTGTTTTGCCATGAGCCATGCCGTCCCCTGCACCAGTTGGCCACTGATTCCGCCTTCTCCCTGGA
CAAA

Alignment

ORF - retro_pcap_462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.01 %
• Parental protein coverage: 70.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TLTCRDCQLNAHKDHQYQFLEDAVRNQRKLLASLVKRLGDKHATLQKSTKEVRS-IRHVSDVQ-KRVQVD
          TLTCRDCQLNAHKDHQYQFLEDAVRNQRKLLA.LVKRLGDKHATL.KSTKEVRS.IRHV.DVQ...VQVD
Retrocopy TLTCRDCQLNAHKDHQYQFLEDAVRNQRKLLALLVKRLGDKHATLRKSTKEVRSSIRHV*DVQ<EHVQVD

Parental  VKMAILQIMKELNKRGRVLVNDAQKVTEGQQ-ERLERQHWTMTKIQKHQE-HILRFASWALESDNNTALL
          VKMAILQIMKELNKRGR.LVNDAQKVTE.QQ.ERLE.QHWTMTKIQKH...HILRFASWALESDNNTALL
Retrocopy VKMAILQIMKELNKRGRMLVNDAQKVTERQQ<ERLECQHWTMTKIQKHKV>HILRFASWALESDNNTALL

Parental  LSKKLIYFQLHRALKMIVDPVEPHGEMKFQWDLNAWTKSAEAFGKIVAERSGTNSTGPAPMAPPRAPGPL
          LSKKLI.FQLHRALKMIVDPVEPHGEMKFQWDL.AWTKSAEAFGKIVAER.GTNSTGPAPMAPPR.PGPL
Retrocopy LSKKLIDFQLHRALKMIVDPVEPHGEMKFQWDLSAWTKSAEAFGKIVAERWGTNSTGPAPMAPPRVPGPL

Parental  SKQGSGSSQPMEVQEG-YGFGSVDDPYSSAEPHVSGVKRSRSGEGEVSGLMRKVPRVSLERLDLDLTADS
          .KQGSGSSQPMEVQEG..GFGS.DDPYSSAEPHV.GVKRS.SGEGEVSGLMRKV..VSLERLDLDLTADS
Retrocopy NKQGSGSSQPMEVQEG>NGFGS-DDPYSSAEPHVWGVKRSCSGEGEVSGLMRKVALVSLERLDLDLTADS

Parental  QPPVFKVFPGNTTEDYNLIVIERGGAAAAAAGQPGTAPPGAPGAPPLPGMAIVKEEETEAAIGAPPAAAE
          QPP...VFPGNTTED.NLIVIERGGAAAAAAGQPGTAPPGAPGAPPLPGMAIVKEEETEAA.GAPPAAAE
Retrocopy QPPILNVFPGNTTEDGNLIVIERGGAAAAAAGQPGTAPPGAPGAPPLPGMAIVKEEETEAATGAPPAAAE

Parental  GPETKPVLMALAEGPGAEGPRLASPSGSTSSGLEVVAPEGASAPSGGPGTLDDSATICRVCQKPGDLVMC
          GPETKPVLMALAEGPGAEG.RLASPSGSTSSGLEVVAPEGASAPSG..GT.DDSATICR.CQ.PGDLVMC
Retrocopy GPETKPVLMALAEGPGAEGSRLASPSGSTSSGLEVVAPEGASAPSGSAGTPDDSATICRICQQPGDLVMC

Parental  NQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDGSLNLDEADTTGVVAKLSPANQRKCERVLLA
          NQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDGSLNLDEADTT.VVAKLSPANQ.KCERVLLA
Retrocopy NQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDGSLNLDEADTTSVVAKLSPANQWKCERVLLA

Parental  LFCHEPCRPLHQLATDSTFSLDQ
          LFCHEPCRPLHQLATDS.FSLD.
Retrocopy LFCHEPCRPLHQLATDSAFSLDK

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_462 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005745	1 retrocopy	retro_cpor_84,
Procavia capensis	ENSPCAG00000007149	1 retrocopy	retro_pcap_462 ,
Rattus norvegicus	ENSRNOG00000027487	1 retrocopy	retro_rnor_1002,