RetrogeneDB ID: retro_chof_1012

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_183735:3965..4193(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEDD8
• Ensembl ID: ENSCHOG00000001228
• Aliases: None
• Description: neural precursor cell expressed, developmentally down-regulated 8 [Source:HGNC Symbol;Acc:7732]

Sequence

>retro_chof_1012
ATGCAGATCTTCGTGAAGACCCTGACCGGCAAGACCATCACCCTGGAGGTAGAGCCCAGTGACACCATCGAGAACGTCAA
GGCCAAGATCCAGGATAAGGAGGGCATTCCCCCTGACCAGCAGAGGCTCATCTTCGCTGGCAAGCAGCTGGAGGATGGCC
GCACTCTGTCTGATTACAACATCCAGAAAGAGTCCACCCTGCACCTGGTCCTGCGCCTCCGGGGTGGC

Alignment

ORF - retro_chof_1012 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.89 %
• Parental protein coverage: 93.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLV
          M.I.VKTLTGK.I....EP.D..E..K.....KEGIPP.QQRLI..GKQ..D..T..DY.I...S.LHLV
Retrocopy MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV

Parental  LALRGG
          L.LRGG
Retrocopy LRLRGG

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_1012 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038842	1 retrocopy	retro_btau_89,
Canis familiaris	ENSCAFG00000012097	1 retrocopy	retro_cfam_1789,
Choloepus hoffmanni	ENSCHOG00000001228	5 retrocopies	retro_chof_1012 , retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus	ENSCJAG00000006876	1 retrocopy	retro_cjac_4064,
Cavia porcellus	ENSCPOG00000010930	1 retrocopy	retro_cpor_371,
Erinaceus europaeus	ENSEEUG00000011640	2 retrocopies	retro_eeur_165, retro_eeur_43,
Echinops telfairi	ENSETEG00000018391	2 retrocopies	retro_etel_1118, retro_etel_1677,
Homo sapiens	ENSG00000129559	1 retrocopy	retro_hsap_180,
Gorilla gorilla	ENSGGOG00000016105	1 retrocopy	retro_ggor_261,
Macaca mulatta	ENSMMUG00000029409	1 retrocopy	retro_mmul_2236,
Monodelphis domestica	ENSMODG00000003254	1 retrocopy	retro_mdom_1681,
Vicugna pacos	ENSVPAG00000009104	4 retrocopies	retro_vpac_270, retro_vpac_316, retro_vpac_480, retro_vpac_558,