RetrogeneDB ID: retro_chof_42

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_248899:1476..2013(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000013271
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000009884
• Aliases: None
• Description: None

Sequence

>retro_chof_42
GCCGACCTGAAGGTGGAGTGTGATGCCTTTGAAGAGAAGATCACAGCTGCAGGCGGGATTGAGCTGTTTGTTGGAGGCAT
TGGCCCCGATGGACATATTGTCTTTAATGAACCGGGCTCCAGTCTGGTTTCTAGGACCCGTGTGAAGACACTGGCCATGG
ACACCATCCTGGCCAATGCCAGGTTCTTCGATGGAGATCTCACCAAGGTGCTCACCATGGCCCTGACGGTGGGCGTGGGC
ACCATCATGGATGCTAGAGAGGTGATGATCCTCATCACAGGTGCACACAAGGCATTTGCTCTGTACAAGGCCATTGAGGA
GGGGGTGAGCCACATGTGGACCGTGTCTGCCTTCCAGCAGCATCCCCGCACAGTGTTTGTGTGTGACGAGGATGCCACCC
TAGAGCTGAAAGTGAAGACTGTCAAGTATTTCAAAGGTTTAACGCTTGTTCATAACAAGTTGGTGGATCCCTTGTACAGT
ATCAAAGAGAAGGAAACAGAGAAAAGCCAGTCTTCTAAGACACCATACAGTGATTAG

Alignment

ORF - retro_chof_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.31 %
• Parental protein coverage: 61.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADLKVECDAFEEKITAAGGIELFVGGIGPDGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGDLTKV
          ADLKVECDAFEEKITAAGGIELFVGGIGPDGHI.FNEPGSSLVSRTRVKTLAMDTILANARFFDGDLTKV
Retrocopy ADLKVECDAFEEKITAAGGIELFVGGIGPDGHIVFNEPGSSLVSRTRVKTLAMDTILANARFFDGDLTKV

Parental  PTMALTVGVGTIMDAREVMILITGAHKAFALYKAIEEGVSHMWTVSAFQQHPRTVFVCDEDATLELKVKT
          .TMALTVGVGTIMDAREVMILITGAHKAFALYKAIEEGVSHMWTVSAFQQHPRTVFVCDEDATLELKVKT
Retrocopy LTMALTVGVGTIMDAREVMILITGAHKAFALYKAIEEGVSHMWTVSAFQQHPRTVFVCDEDATLELKVKT

Parental  VKYFKGLMLVHNKLVDPLYSIKEKETEKSQSSKTPYSD
          VKYFKGL.LVHNKLVDPLYSIKEKETEKSQSSKTPYSD
Retrocopy VKYFKGLTLVHNKLVDPLYSIKEKETEKSQSSKTPYSD

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_42 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007865	1 retrocopy	retro_btau_535,
Choloepus hoffmanni	ENSCHOG00000009884	2 retrocopies	retro_chof_2278, retro_chof_42 ,
Dasypus novemcinctus	ENSDNOG00000007804	3 retrocopies	retro_dnov_1363, retro_dnov_1608, retro_dnov_508,
Macropus eugenii	ENSMEUG00000015442	1 retrocopy	retro_meug_655,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337,
Mus musculus	ENSMUSG00000052102	1 retrocopy	retro_mmus_2711,
Oryctolagus cuniculus	ENSOCUG00000016963	1 retrocopy	retro_ocun_1266,
Otolemur garnettii	ENSOGAG00000007303	3 retrocopies	retro_ogar_2251, retro_ogar_2506, retro_ogar_446,
Ictidomys tridecemlineatus	ENSSTOG00000016508	1 retrocopy	retro_itri_1135,
Tupaia belangeri	ENSTBEG00000003330	2 retrocopies	retro_tbel_2431, retro_tbel_59,