RetrogeneDB ID: retro_chof_1928

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_42482:1155..1533(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG5
• Ensembl ID: ENSCHOG00000006399
• Aliases: None
• Description: autophagy related 5 [Source:HGNC Symbol;Acc:589]

Sequence

>retro_chof_1928
TTGCTTTTGCCAAGAGTAAGTTATTTGATGTTGGTAACTGACAAAGTGAAAAAGCACTTTCAGAAGGTTATGAGACAAGA
AGACATTAGTGAGATATGGTTTAAATATGAAGGCACACCACTGAAATGGCGTTATCCAATTGGTTTGCTATTTGATCTTC
TTACATCAAGTTCTACTCTTCCTTGGAACATCACAGTACATTTTAAGAGTTTTCCAGAAAAGGACCTTCTACACTGTCCA
TCTTAGGATGCAATTGAAGCTCATTTTATGTCTTGTATGAAAGAAGCTGATGCTTTAAAGCATAAAAGTCAAGTAATCAA
TGAAACGCAAAAAAAAGATCATAAGCAGCTCTGGATGGGATTACAAAATGGTAAATAC

Alignment

ORF - retro_chof_1928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.3 %
• Parental protein coverage: 52.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPGNITVRFKS
          LLLPRVSYL.LVTDKVKKHFQKVMRQEDISEIWF.YEGTPLKW.YPIGLLFDLL.SSS.LP.NITV.FKS
Retrocopy LLLPRVSYLMLVTDKVKKHFQKVMRQEDISEIWFKYEGTPLKWRYPIGLLFDLLTSSSTLPWNITVHFKS

Parental  FPEKDLLHCPSKDAIEAHFMSCMKEADAFKHKSQVINEMQKKDHKQLWMGLQNDRF
          FPEKDLLHCPS.DAIEAHFMSCMKEADA.KHKSQVINE....DHKQLWMGLQN...
Retrocopy FPEKDLLHCPS*DAIEAHFMSCMKEADALKHKSQVINETXXXDHKQLWMGLQNGKY

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_1928 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006399	1 retrocopy	retro_chof_1928 ,
Dasypus novemcinctus	ENSDNOG00000013004	2 retrocopies	retro_dnov_1805, retro_dnov_950,
Myotis lucifugus	ENSMLUG00000014090	1 retrocopy	retro_mluc_872,
Ictidomys tridecemlineatus	ENSSTOG00000016507	1 retrocopy	retro_itri_1724,