RetrogeneDB ID: retro_chof_2129

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_51875:6086..6589(+)
• 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_2129
ATGACCAACTTCAAGTATCAGGAGCTGCAAGATGAGAAGGAACCCAGAGTTGCTAAAATTCATGTCTTATGTTTCTAAAG
GGAATTTTATGATGTGTTTAATGTTGTCTTGCTATTACATAATGAAGACAATTTTCTCAAAGAGGGGGCATCACATGCAT
TTCCCAATATAACATGGATCAGTCCTCGTAGTGAAGATAGAAGAATATGAAGGTCAGGTTTTAATTACAGAATACGGCGA
CATGGTCGTAGAAGATTTTTGGATCCCAGAAACAAAATTAATTGTGTTTTCTCACTTAGAGAAGGAAGAATATGACCCTT
AATGAAAGGTTATAGGTGGGGATCTGAGATATTGGAGAGAATTCTGCGACAGTATGCTCAGTGTTACATGAGAGATTATT
ATTCTAATGTCTTCTATACTGTTCATGCTATAGCTATATATGGACAGCTGACTTCTTTTACATTTATTGAAAGTTTCCAG
TTCTGACCTAAAAACTTTGGAAT

Alignment

ORF - retro_chof_2129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.27 %
• Parental protein coverage: 70.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAF-AQYNMDQFT-PVKIE
          M..F.......EK....AK........EF..VFN.V.LL.N.DN.L.EGA.HAF..QYNMDQ....VKIE
Retrocopy MTNFKYQELQDEKEPRVAKIHVLCF*REFYDVFNVVLLLHNEDNFLKEGASHAF<SQYNMDQSS<VVKIE

Parental  GYDDQVLITEHGDL-GNSRFLDPRNKVSFKFDHLR-KEASDPQPEEVDGGLKSWRESCDSAL-RAYVKDH
          .Y..QVLITE.GD..G..RFLDPRNK....F..LR.KE..DP......G.L..WRE.CDS.L...Y..D.
Retrocopy EYEGQVLITEYGDM<GRRRFLDPRNKINCVFS-LR>KEEYDP**KVIGGDLRYWREFCDSML<QCYMRDY

Parental  YSNGFCTVYAKTIDGQQTIIACIESHQFQPKNF-WN
          YSN.F.TV.A..I.GQ.T....IES.QF.PKNF.WN
Retrocopy YSNVFYTVHAIAIYGQLTSFTFIESFQF*PKNF<WN

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_2129 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,