RetrogeneDB ID: retro_pcap_463

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_99824:752..1333(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLB
• Ensembl ID: ENSPCAG00000007734
• Aliases: None
• Description: polymerase (DNA directed), beta [Source:HGNC Symbol;Acc:9174]

Sequence

>retro_pcap_463
TATTTTGAGGACTTTCAGAAAAGAATCCCTCGTGAAGAGATGTTACAGATGCAGGATATCGTGCTGAACGAAGTTAAAAG
AGTGGATTCTGAATACATTACTACAGTCTGTGGAAGTTTTAGGAGAGGTGCAGAGTCCAGTGGTGACATGGACGTTCTGT
TGACCCTTCCGAACTTTACTTCTGAGTCAGCCAAACAGCCAAAACTGTTACACCGAGTTTTGGAGCAGTTACAGAAGGTC
CATTTTATTACAGACACTTTGTCAAAGGGTGAAACAAAGTTCATGGGTATTTGCCAGCTTCCCAGTAAAACAATGAAAAA
GAGTATCCACACAGGAGAACTGATATCAGGTTAATACCCGAGGATCAGTATTACTGTGGTGTGCTCTACTTCACTGGGAG
TGATATTTTCAATAAGAACATGAGGGCTAACGCCCTAGATAAGGGCTTTACAATAAACGAATACACAATCCGGCCCTTGG
GAGTCACCAAAGTTGCTGGAGAACCCCTACCTGTGGATAGTGAGAAAGATATCTTTGACTACATCCAGTGGAAATACTGA
GAACCCAAGGACCGAAGTGAG

Alignment

ORF - retro_pcap_463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.85 %
• Parental protein coverage: 58.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YFEDFEKRIPREEMLQMQDIVLNEVKRVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESAKQPKLL
          YFEDF.KRIPREEMLQMQDIVLNEVKRVDSEYI.TVCGSFRRGAESSGDMDVLLT.P.FTSESAKQPKLL
Retrocopy YFEDFQKRIPREEMLQMQDIVLNEVKRVDSEYITTVCGSFRRGAESSGDMDVLLTLPNFTSESAKQPKLL

Parental  HRVVEQLQKVHFITDTLSKGETKFMGVCQLPSK-NNEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNK
          HRV.EQLQKVHFITDTLSKGETKFMG.CQLPSK.NNEKEYPHRR.DIRLIP.DQYYCGVLYFTGSDIFNK
Retrocopy HRVLEQLQKVHFITDTLSKGETKFMGICQLPSK<NNEKEYPHRRTDIRLIPEDQYYCGVLYFTGSDIFNK

Parental  NMRAHALDKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
          NMRA.ALDKGFTINEYTIRPLGVT.VAGEPLPVDSEKDIFDYIQWKY.EPKDRSE
Retrocopy NMRANALDKGFTINEYTIRPLGVTKVAGEPLPVDSEKDIFDYIQWKY*EPKDRSE

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_463 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005134	1 retrocopy	retro_amel_1482,
Canis familiaris	ENSCAFG00000005517	1 retrocopy	retro_cfam_891,
Echinops telfairi	ENSETEG00000002644	1 retrocopy	retro_etel_37,
Macropus eugenii	ENSMEUG00000012619	1 retrocopy	retro_meug_1007,
Procavia capensis	ENSPCAG00000007734	1 retrocopy	retro_pcap_463 ,