RetrogeneDB ID: retro_chof_1826

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_395885:249..822(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRR1
• Ensembl ID: ENSCHOG00000009636
• Aliases: None
• Description: KRR1, small subunit (SSU) processome component, homolog (yeast) [Source:HGNC Symbol;Acc:5176]

Sequence

>retro_chof_1826
GAAGCAGAACTCCTCACTGTTCCTCATGGTTGGAAGGAACCAGCCTTTTCGAAAGAGGATAACCCCAGAGGGCTCCTAGA
GGAAAGCAGTTTTGCAACTTTGTTTCCAAAATATAGGGAGGCTTACTTGAAAGAATGCTGGCTATTGGTGCAGAAAGCCT
TGAATGAAGATCACATTAATGCAACCCTGGACCAGATTGAGGGCGGCATGACGGTATGACAGTTTACACAAGAAGACTTT
TGATCCATACATCATCATTAGGGCCAGAGGCCTAACAAAACTTTTAGCAAGGAGCACATCATTTGAACAGACAGTCTGAA
TTCTTCAGGGTGATGTTGCTTGTGACATCATTAAAACAGGTTCTTTAGTATGAAATAAAGAAAGGTTTGTTAAAAGAAGG
CAACAGCTTATTGGTCTCAAAGGATCCACACTGAAGGCATTGTAACTCTTAATAAACTTTTACATGATGGTTCAGGTAAA
CACAGTTTCAGCCATTGGACACTTTAGTGGCTTAAAGAAGTTTGAAAATAAGTCTTAGATACTATGAAGAATATTCATCC
AATGTATAACATT

Alignment

ORF - retro_chof_1826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.9 %
• Parental protein coverage: 53.98 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EAELLTVPDGWKEPAFSKEDNPRGLLEESSFATLFPKYREAYLKECWPLVQKALNEHHINATLDLIEGSM
          EAELLTVP.GWKEPAFSKEDNPRGLLEESSFATLFPKYREAYLKECW.LVQKALNE.HINATLD.IEG.M
Retrocopy EAELLTVPHGWKEPAFSKEDNPRGLLEESSFATLFPKYREAYLKECWLLVQKALNEDHINATLDQIEGGM

Parental  TV-YTTKKTF-DPYIIIRARDLIKLLARSVSFEQAVRILQDDIACDIIKIGSLVRNKERFVKRRQRLIGP
          TV...T...F.DPYIIIRAR.L.KLLARS.SFEQ.V.ILQ.D.ACDIIK.GSLV.NKERFVKRRQ.LIG.
Retrocopy TV*QFTQEDF>DPYIIIRARGLTKLLARSTSFEQTV*ILQGDVACDIIKTGSLV*NKERFVKRRQQLIGL

Parental  KGSTLKALELLTNCYIMVQGNTVSAIGPFSG-LKEVRKVVLDTMKNIHPIYNI
          KGSTLKAL.LL.N.Y.MVQ.NTVSAIG.FSG.LKEV.K.VLDTMKNIHP.YNI
Retrocopy KGSTLKAL*LLINFYMMVQVNTVSAIGHFSG<LKEV*K*VLDTMKNIHPMYNI

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_1826 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 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006437	1 retrocopy	retro_amel_1292,
Canis familiaris	ENSCAFG00000005665	1 retrocopy	retro_cfam_1091,
Choloepus hoffmanni	ENSCHOG00000009636	5 retrocopies	retro_chof_1030, retro_chof_1826 , retro_chof_2438, retro_chof_2452, retro_chof_365,
Monodelphis domestica	ENSMODG00000020451	1 retrocopy	retro_mdom_791,
Tupaia belangeri	ENSTBEG00000008145	5 retrocopies	retro_tbel_1056, retro_tbel_2060, retro_tbel_2911, retro_tbel_2915, retro_tbel_3679,