RetrogeneDB ID: retro_chof_1062

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_192057:2629..3090(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN7C
• Ensembl ID: ENSCHOG00000000111
• Aliases: None
• Description: lin-7 homolog C (C. elegans) [Source:HGNC Symbol;Acc:17789]

Sequence

>retro_chof_1062
GCGCTGGGGGAACCTGTGAGGCTGGAGAGAGATATTTGTAGAGCAATTGAATTGTTGGAAAAACTGCAAAGGAGTGGAGA
AGTACCACCACAAAAACTTCAGGCTTTACAAAGAGTCCTTTAAAGTGAGTTCTGTGATGCTGTAAGAGAGGGATATGAAC
ACATCTATGAAACTGTGGACATCAGTAGCAGTCCTGAAGTGAGAGCTAATGCAAATGCAAAGGCTACAGTCGCTGCGTTT
GCTGCCAGTGAAGGACATTCTCATCCTCGAGTGGTTGAGCTACCAAAAACAGAAGAGGGCCTTGGATTTAATATTATGTG
AGGGAAAGAACAAAACTCTCCAATCTATATATCTCGAATAATTCCAGGCGGTATTGCTGATAGACATGGGGGCGTCAAAT
GAGACCACCTCTTTCTGTTAATGGAGTGAGCGCTGAAGGAGAACATCATGAAAAAGCTGTA

Alignment

ORF - retro_chof_1062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 78.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALGEPVRLERDICRAIELLEKLQRSGEVPPQKLQALQRVLQSEFCNAVREVYEHVYETVDISSSPEVRAN
          ALGEPVRLERDICRAIELLEKLQRSGEVPPQKLQALQRVL.SEFC.AVRE.YEH.YETVDISSSPEVRAN
Retrocopy ALGEPVRLERDICRAIELLEKLQRSGEVPPQKLQALQRVL*SEFCDAVREGYEHIYETVDISSSPEVRAN

Parental  ATAKATVAAFAASEGHSHPRVVELPKTEEGLGFNIMGGKEQNSPIYISRIIPGGIADRHGGLKRGDQL-L
          A.AKATVAAFAASEGHSHPRVVELPKTEEGLGFNIM.GKEQNSPIYISRIIPGGIADRHGG....D.L.L
Retrocopy ANAKATVAAFAASEGHSHPRVVELPKTEEGLGFNIM*GKEQNSPIYISRIIPGGIADRHGGV-K*DHL<L

Parental  SVNGVSVEGEHHEKAV
          SVNGVS.EGEHHEKAV
Retrocopy SVNGVSAEGEHHEKAV

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_1062 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 2 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000111	7 retrocopies	retro_chof_1046, retro_chof_1062 , retro_chof_1417, retro_chof_2399, retro_chof_2401, retro_chof_2515, retro_chof_864,
Microcebus murinus	ENSMICG00000005165	2 retrocopies	retro_mmur_1590, retro_mmur_577,