RetrogeneDB ID: retro_chof_400

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_104147:2293..3190(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000000166
• Aliases: None
• Description: None

Sequence

>retro_chof_400
ATGGCCACCTTCGTGGAACTCAGTACCAAAGCCAAGATGCCCATCGTGGGACTTGGCACCTGGAAGTCTCCTCCAGGCAA
AGTCAAAGAGGCTGTGAAGGCAGCAATTGACATAGGATATCGCCACATCGACTGTGCCTATGCCTACAGGAATGAGAACG
AGGTCGGGGAAGCTATCCAGGAGAAGATCCAAGAGGAAGTTGTTAAGCGGGAGGACCTCTTCATCATTACCAAGTTATGG
CTCACCTTCTTTGAGAGGTCCCTCGTGAAGGAATGCTGCAAGAAGACCCTCAAGGATCTGAAACTGGACTATCTCGACAT
CTATGTTATTCACTTTCCACAGGGATTACAGGCTGGTAAGGACTGGTTCCCTAAAGATGACAAAGGCAATGCTATCCCCA
GTAAAGCAACATTCTTGGAAACCTGGGAGGCCATGGAAGAGCTGGTGGATGAGGGGCTGGTGAAAGCCATTGGGATCTCC
AATTTCAACCACTTCCAAACTGAAAGGCTCTTGAACAAACCTGGACTGAAACATAAACCAGCGACTAACCAGATTGAGTG
TCACCCATACCTGAAGCAGGAGAAACTGATCCAGTACTGCCACTCCAAGGGCATCACAGTCACTGCCTACAGCCCCCTGG
GTTCTCCAGATAGACCTTGGGCCAAGCCAGGGGACCCTTCACTACTAGAGGATCCCCAAATTAAGGAGATTGCAGCAAAG
CACAATAAAACCACTGCCCAGGTTCTGATCTGGTTCCATATCCAGAGGAATGTGCCCGTGATCCCCAAGTCTGTGACTCT
CCAACGCATTGCTGAGAACTTTAAGGTCTTTGACTTTAAATTGAGTGATGAGGAGATGGCGACCATACTCACCTTCAACA
GAAACTGGAGGGCCTGT

Alignment

ORF - retro_chof_400 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.29 %
• Parental protein coverage: 99.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATFAELSTKAKMPIVGLGTWKSPPGKVKEAVKAAIDIGYRHIDCACAYRNEDEVGEAIQEKIQEKVVKR
          MATF.ELSTKAKMPIVGLGTWKSPPGKVKEAVKAAIDIGYRHIDCA.AYRNE.EVGEAIQEKIQE.VVKR
Retrocopy MATFVELSTKAKMPIVGLGTWKSPPGKVKEAVKAAIDIGYRHIDCAYAYRNENEVGEAIQEKIQEEVVKR

Parental  EDLFIVSKLWLTFFERSLVKECCKKTLKDLKLDYLDIYLIHFPQGLQAGKDWFPKDDKGNAIPSKATFLE
          EDLFI..KLWLTFFERSLVKECCKKTLKDLKLDYLDIY.IHFPQGLQAGKDWFPKDDKGNAIPSKATFLE
Retrocopy EDLFIITKLWLTFFERSLVKECCKKTLKDLKLDYLDIYVIHFPQGLQAGKDWFPKDDKGNAIPSKATFLE

Parental  TWEAMEELVDEGLVKAIGISNFNHFQIERLLNKPGLKYKPVTNQIKCHTYHMQEKLIQYCHSKGITVTAY
          TWEAMEELVDEGLVKAIGISNFNHFQ.ERLLNKPGLK.KP.TNQI.CH.Y..QEKLIQYCHSKGITVTAY
Retrocopy TWEAMEELVDEGLVKAIGISNFNHFQTERLLNKPGLKHKPATNQIECHPYLKQEKLIQYCHSKGITVTAY

Parental  RPLGSPDL-WAKPGDPSLLEDPKNKEIAAKHKKTTAQVLIRCHIQRKVAGIPKSVTPQRSTENFQVFDFN
          .PLGSPD..WAKPGDPSLLEDP..KEIAAKH.KTTAQVLI..HIQR.V..IPKSVT.QR..ENF.VFDF.
Retrocopy SPLGSPDRPWAKPGDPSLLEDPQIKEIAAKHNKTTAQVLIWFHIQRNVPVIPKSVTLQRIAENFKVFDFK

Parental  LSDEKMTTILSFKRNWRTC
          LSDE.M.TIL.F.RNWR.C
Retrocopy LSDEEMATILTFNRNWRAC

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_400 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 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400 ,
Choloepus hoffmanni	ENSCHOG00000008668	1 retrocopy	retro_chof_568,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,