RetrogeneDB ID: retro_chof_772

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_14661:5642..6092(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000002224
• Aliases: None
• Description: None

Sequence

>retro_chof_772
ATGGCCTCAGGCGCCGCCACCACAGCCATGAAGATTGCAATAATTGGCGAAACAGGCCTGGATGATCCAGAAATTTTAGA
AGGAAGAACCGAAAAATATGTGGATACTCCATTTGGCAAGCCATCTGATGCCTTAATTTTGGGGAAGATAAAAAAATGTC
GCTTGTTTCCTTCTTGCAAGGCACGGGAGGCAGCACACCATCACGCCTTCAGAAGTCAACTACCAGGCGAACATCTGGGC
CTTGAAGGAGGCGGGCTGCGCTCAGGTCATAACGGCCACGGCTTGTGGCTCCTTGAGGGAGGACGTCCAGCCCGGCGATA
TTGTCATTATCGATCAGTTCATCGACAGGACCACCAAAAGGCCTCAGACTTTCTATGATGGAAGTCATTCCTGTGCCAGA
GGAGTGTGCCATATTCCAATGGCTGAGCATTCTGTCCTAAAACGAGAGAG

Alignment

ORF - retro_chof_772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.24 %
• Parental protein coverage: 53.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPGAATIAVKVGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKIK-NVDCVLLARHGRQHTIMP
          MA.GAAT.A.K..IIG.TGLDDPEILEGRTEKYVDTPFGKPSDALILGKIK.NV.C.LLARHGRQHTI.P
Retrocopy MASGAATTAMKIAIIGETGLDDPEILEGRTEKYVDTPFGKPSDALILGKIK>NVACFLLARHGRQHTITP

Parental  SEVNHQANIWALKEEGCTHIVVTTACGSLREEIQPGDMVIIDQFIDRTTKSPQPFYDGSHSCARGVCHIT
          SEVN.QANIWALKE.GC......TACGSLRE..QPGD.VIIDQFIDRTTK.PQ.FYDGSHSCARGVCHI.
Retrocopy SEVNYQANIWALKEAGCAQVITATACGSLREDVQPGDIVIIDQFIDRTTKRPQTFYDGSHSCARGVCHIP

Parental  MAE-PLCPKTRE
          MAE...CPKTRE
Retrocopy MAE<AFCPKTRE

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_772 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025929	1 retrocopy	retro_btau_1049,
Choloepus hoffmanni	ENSCHOG00000002224	1 retrocopy	retro_chof_772 ,
Callithrix jacchus	ENSCJAG00000008021	2 retrocopies	retro_cjac_187, retro_cjac_950,
Cavia porcellus	ENSCPOG00000000825	1 retrocopy	retro_cpor_375,
Dasypus novemcinctus	ENSDNOG00000008670	1 retrocopy	retro_dnov_1572,
Echinops telfairi	ENSETEG00000013214	1 retrocopy	retro_etel_588,
Macropus eugenii	ENSMEUG00000015381	2 retrocopies	retro_meug_807, retro_meug_917,
Microcebus murinus	ENSMICG00000015072	1 retrocopy	retro_mmur_927,
Macaca mulatta	ENSMMUG00000001137	1 retrocopy	retro_mmul_1549,
Ornithorhynchus anatinus	ENSOANG00000013963	1 retrocopy	retro_oana_38,
Oryctolagus cuniculus	ENSOCUG00000012289	2 retrocopies	retro_ocun_1355, retro_ocun_341,
Otolemur garnettii	ENSOGAG00000007889	1 retrocopy	retro_ogar_3285,
Ochotona princeps	ENSOPRG00000001259	1 retrocopy	retro_opri_792,