RetrogeneDB ID: retro_chof_1008

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_183426:157..863(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSCHOG00000004131
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]

Sequence

>retro_chof_1008
ATGGCGGATCGGGAGGAGCAGTTGTCTGATGAGGGGAAGGTGCATAAAGCAGCAAAATTCATCCTTCATGCCCCTCCTGG
AGAATTTAATGAGGTGTTTAGTGATGTTCGGTTACTGCTTAACAACGATAATCTTCTCAGGGAAGGAGCAGCTCATGCAT
TTGTACAGTATGACTTGGACCAGTTTACTCCAGTAAAAATTGAGGGTTATGAAGATCAGGTATTGATAACAGAACATGGC
CACTTGGCAGATGGAAAGTTTCTGGATCCCCAAACAGAATCTGTTTCAAATTTGATCACTTAAGAAAGGAAGCAACTGAT
CCAAGACCCTATGAAGCAGAATCATGGAGAACTTCCATAGAAATTGCTCTGCGAGTTTATGTAAAAGAACATTACCTGAA
TGGAGTGTGCACTGTGTATGGGAAAAAAAATAGATGGACAGCAAACCATTATTGCATGCACAGAAAGCCATCAGTTCCAA
GCAAAAAACTTCTGGAATGGTCAATAGAGGTCAGAGTGGAAGTTTACAATCAATTCTCCAACCTCTCAAGTGGCTGGCAT
CTTGAAAATTCAGATTCATTATTACGAAGCTGGTAATGTTCAGCTAGTGAGTCATAAAGATATACAAGATTTCCTAACAG
TGTCTAATGAGGTACAAACAGAAAAGAATTTATGAAGATAAGAGAGTCTGAGAAAATAAATACCAG

Alignment

ORF - retro_chof_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGY
          MAD.E...SDE.KV..AAKFI.HAPPGEFNEVF.DVRLLLNNDNLLREGAAHAF.QY..DQFTPVKIEGY
Retrocopy MADREEQLSDEGKVHKAAKFILHAPPGEFNEVFSDVRLLLNNDNLLREGAAHAFVQYDLDQFTPVKIEGY

Parental  DDQVLITEHGDLGNSRFLDPR-NKVSFKFDHLRKEASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSNG
          .DQVLITEHG.L....FLDP..N...FKFDHLRKEA.DP.P.E......SWR.S...ALR.YVK.HY.NG
Retrocopy EDQVLITEHGHLADGKFLDPQ<NRICFKFDHLRKEATDPRPYEAE----SWRTSIEIALRVYVKEHYLNG

Parental  FCTVYA-KTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVS
          .CTVY.....DGQQTIIAC.ESHQFQ.KNFWNG..RSEWKFTI..PT.QV.G.LKIQ.HYYE.GNVQLVS
Retrocopy VCTVYG>XXXDGQQTIIACTESHQFQAKNFWNGQ*RSEWKFTINSPTSQVAGILKIQIHYYEAGNVQLVS

Parental  HKDVQDSISVSNEVQT-AKEFIKIIEHA-ENEYQ
          HKD.QD...VSNEVQT..KEF.KI.E...EN.YQ
Retrocopy HKDIQDFLTVSNEVQT<RKEFMKIRESE<ENKYQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1008 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Choloepus hoffmanni	ENSCHOG00000004131	8 retrocopies	retro_chof_1008 , retro_chof_1419, retro_chof_1499, retro_chof_1704, retro_chof_1861, retro_chof_2129, retro_chof_625, retro_chof_711,
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Ictidomys tridecemlineatus	ENSSTOG00000015956	1 retrocopy	retro_itri_1044,