RetrogeneDB ID: retro_chof_1888

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_41556:11352..11685(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRB
• Ensembl ID: ENSCHOG00000007884
• Aliases: None
• Description: ubiquinol-cytochrome c reductase binding protein [Source:HGNC Symbol;Acc:12582]

Sequence

>retro_chof_1888
ATGGCGGGCTGCCCCGCTGTTGCAGCATCAGGCCGGTGGCTGGATGATATTCGAAAATGATATTACAGTGCTGCAGGGTT
CAATAAACTGGGGTTAATGAGAGATGATACAATAGCTGAGAATGAAGATACAGAAGAAGCCATAAGAAGGCTTCCTGAGA
ACCTTTATAATGACAGGGTGTTTTGCACTAAGAGAGCACTGGACCTGAACATGAGGCAGCAGATCTTGCCTAAAGAGCAG
TGGACAGAATATGAGGAGGATAAATTCTGTCTTGAACCATATGTGAAAGAAGTTATTCGGGAAAGAGAAGAGAGAGAAGA
ATGGGCAAAGAAA

Alignment

ORF - retro_chof_1888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGRPAVAASGRWLDGIRKWYYNAAGFNKLGLMRDDTISENEDVKEAIRRLPENVYNDRVFRIKRALDLS
          MAG.PAVAASGRWLD.IRK.YY.AAGFNKLGLMRDDTI.ENED..EAIRRLPEN.YNDRVF..KRALDL.
Retrocopy MAGCPAVAASGRWLDDIRK*YYSAAGFNKLGLMRDDTIAENEDTEEAIRRLPENLYNDRVFCTKRALDLN

Parental  MKQQILPKEQWTKYEEDKFYLEPYLKEVIRERKEREEWAKK
          M.QQILPKEQWT.YEEDKF.LEPY.KEVIRER.EREEWAKK
Retrocopy MRQQILPKEQWTEYEEDKFCLEPYVKEVIREREEREEWAKK

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_1888 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 12 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001521	3 retrocopies	retro_btau_1641, retro_btau_374, retro_btau_417,
Choloepus hoffmanni	ENSCHOG00000007884	22 retrocopies	retro_chof_1256, retro_chof_1271, retro_chof_1468, retro_chof_1662, retro_chof_1888 , retro_chof_2017, retro_chof_2170, retro_chof_2332, retro_chof_2528, retro_chof_2536, retro_chof_2554, retro_chof_257, retro_chof_2684, retro_chof_394, retro_chof_524, retro_chof_599, retro_chof_635, retro_chof_654, retro_chof_699, retro_chof_766, retro_chof_773, retro_chof_975,
Equus caballus	ENSECAG00000009780	1 retrocopy	retro_ecab_1116,
Latimeria chalumnae	ENSLACG00000004465	1 retrocopy	retro_lcha_127,
Loxodonta africana	ENSLAFG00000002542	1 retrocopy	retro_lafr_727,
Nomascus leucogenys	ENSNLEG00000026670	1 retrocopy	retro_nleu_1357,
Pteropus vampyrus	ENSPVAG00000012321	1 retrocopy	retro_pvam_498,
Rattus norvegicus	ENSRNOG00000024967	1 retrocopy	retro_rnor_290,
Ictidomys tridecemlineatus	ENSSTOG00000008017	1 retrocopy	retro_itri_46,
Tupaia belangeri	ENSTBEG00000002453	28 retrocopies	retro_tbel_1046, retro_tbel_1268, retro_tbel_1357, retro_tbel_1568, retro_tbel_1583, retro_tbel_1656, retro_tbel_1688, retro_tbel_169, retro_tbel_1858, retro_tbel_2106, retro_tbel_2217, retro_tbel_248, retro_tbel_2675, retro_tbel_274, retro_tbel_2883, retro_tbel_2885, retro_tbel_2893, retro_tbel_2942, retro_tbel_3129, retro_tbel_3156, retro_tbel_3291, retro_tbel_3492, retro_tbel_3662, retro_tbel_4334, retro_tbel_4539, retro_tbel_457, retro_tbel_517, retro_tbel_784,
Tursiops truncatus	ENSTTRG00000007348	3 retrocopies	retro_ttru_1106, retro_ttru_501, retro_ttru_754,
Drosophila melanogaster	FBgn0030733	1 retrocopy	retro_dmel_22,