RetrogeneDB ID: retro_chof_1221

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_229594:231..1206(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSCHOG00000004191
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 [Source:HGNC Symbol;Acc:2741]

Sequence

>retro_chof_1221
GATCTTCTAGCAGCTGCGAAGACAGGCAGTGGCAAAACCCTGGCATTTCTCATCCCTGCTATTGAACTCATTGTTAAGTT
AAAATTCATGCCCAGGAATGGAACAGGAGTCCTTATTCTCTCACCTACTAGGGAGCTGGCCATGCAGACGTTTGGTGTGC
TTAAGGAGCTAATGACCCACCACGTCCACACATATGGGTTGATAATGGGGGGCAGTAACAGATCTGCTGAAGCACAGAAA
CTTGTTAATGGAATCAACATCATCGTGGCCACGCCAGGTCGACTCCTGGACCATATGCAGAATACCCCAGGGTTTATGTA
TAAAAACCTACAGTGTCTTGTTATTGATGAGGCTGATCGTATCTTGGATGTTGGGTTTGAAGAGGAATTAAAGCAAATTA
TTAAACTTCTGCCAGTACGCAGACAGACCATGCTCTTTTCTGCCACACAAACTCGAAAAGTTGAAGACCTGGCAAGAATT
TCTTTGAAAAAGGAGCCATTGTATGTTGGTGTTGATGATGATAAAACTAATGCAACAGTGGATGGGCTTGAGCAGGGATA
TGTTGTTTGTCCCTCTGAAAAGAGATTCCTTCTGCTCTTTACATTCCTTAAGAAGAACCGAAAGAAGAAAATGATGGTGT
TCTTTTCATCCTGTAAGTCTGTGAAATACCACTACGAGTTGCTGAACTACATCGATTTGCCTGTCTCGGCCATTCATGGA
AAACAGAAGCAAAATAAGCGGACGACCACCTTCTTCCAGTTTTGCAATGCAGATTCAGGGACACTGTTGTGTACAGATGT
GGCAGCTCGAGGGCTGGATATTCCTGAAGTTGACTGGATTGTTCAGTATGACCTTCCAGATGACCCTAAGGAATATATTC
ATCGTGTGGGTAGAACAGCCAGAGGCCTAAATGGAAGAGGACATGCCTTGCTCATTTTGCACCCAGAGGAATTGGGTTTC
CTTCATTATTTGAAG

Alignment

ORF - retro_chof_1221 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 50.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLLAAAKTGSGKTLAFLIPAIELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMG
          DLLAAAKTGSGKTLAFLIPAIELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMG
Retrocopy DLLAAAKTGSGKTLAFLIPAIELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMG

Parental  GSNRSAEAQKLVNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPVR
          GSNRSAEAQKLVNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPVR
Retrocopy GSNRSAEAQKLVNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPVR

Parental  RQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKTNATVDGLEQGYVVCPSEKRFLLLFTFPKKNRRKK
          RQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKTNATVDGLEQGYVVCPSEKRFLLLFTF.KKNR.KK
Retrocopy RQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKTNATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKK

Parental  MMVFFSSCKSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWI
          MMVFFSSCKSVKYHYELLNYIDLPV.AIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWI
Retrocopy MMVFFSSCKSVKYHYELLNYIDLPVSAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARGLDIPEVDWI

Parental  VQYDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLK
          VQYD.PDDPKEYIHRVGRTARGLNGRGHALLIL.PEELGFL.YLK
Retrocopy VQYDLPDDPKEYIHRVGRTARGLNGRGHALLILHPEELGFLHYLK

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_1221 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 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004191	6 retrocopies	retro_chof_1221 , retro_chof_1539, retro_chof_1636, retro_chof_2416, retro_chof_2418, retro_chof_721,
Callithrix jacchus	ENSCJAG00000021414	5 retrocopies	retro_cjac_2309, retro_cjac_2743, retro_cjac_4179, retro_cjac_644, retro_cjac_753,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Ochotona princeps	ENSOPRG00000001701	1 retrocopy	retro_opri_1039,