RetrogeneDB ID: retro_pcap_313

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_32079:14966..15326(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LZTFL1
• Ensembl ID: ENSPCAG00000009783
• Aliases: None
• Description: leucine zipper transcription factor-like 1 [Source:HGNC Symbol;Acc:6741]

Sequence

>retro_pcap_313
GTGTTACTTACGCGGCAGCTTTTCTCATGTGCTAAGAAGTGGTGTCTTAAGTTCTAGACAGATATCTCGGCTGTCTGAAA
ACAGAGAATTGTTAGAACAAGTTGCGGAATTCAAAAAGGTATAATTTACACCTTCAGACAAAAGACTATCTTAGATACCA
TAAAACCAGAACTTGTTCCACTTATGGGAAAAGAGAACAGCACAACTCATGTTAAGGAAACTTTAAGTCTTCAAGAAGAC
AATGAGAAATTGAAGTCAAAGCTGCTGAAGAGTGTTCGAGTACAGGCTACAAACTCAAAGGGTGAGAAGTCAGAACCAGA
AGGAGCACTGCTAGAGTTACAGCTTAATCAAGGAAATCAA

Alignment

ORF - retro_pcap_313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.84 %
• Parental protein coverage: 59.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLLLRQLFSQAEKWYLKLQTDISEL-ENRELLEQVAEFEKAEFTSSNK-KPIADTVKPKLAPLNEGATAE
          VLL.RQLFS.A.KW.LK..TDIS...ENRELLEQVAEF.K..FT.S.K.K.I.DT.KP.L.PL.......
Retrocopy VLLTRQLFSCAKKWCLKF*TDISAV>ENRELLEQVAEFKKV*FTPSDK<KTILDTIKPELVPLMGKENST

Parental  LLNKEILRLQEENEKLKSR-LKTVEIQATNALDEKSKLERTLQDLQLDQGNE
          ...KE.L.LQE.NEKLKS..LK.V..QATN...EKS..E..L..LQL.QGN.
Retrocopy THVKETLSLQEDNEKLKSKLLKSVRVQATNSKGEKSEPEGALLELQLNQGNQ

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_313 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003899	1 retrocopy	retro_chof_1935,
Echinops telfairi	ENSETEG00000013761	1 retrocopy	retro_etel_1726,
Loxodonta africana	ENSLAFG00000010237	1 retrocopy	retro_lafr_155,
Mus musculus	ENSMUSG00000025245	3 retrocopies	retro_mmus_1834, retro_mmus_3266, retro_mmus_3276,
Procavia capensis	ENSPCAG00000009783	1 retrocopy	retro_pcap_313 ,