RetrogeneDB ID: retro_chof_53

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_302444:4..1243(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000013973
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000010454
• Aliases: None
• Description: None

Sequence

>retro_chof_53
ATGGCGCAGCATGACTTTGTTCCTGCTTGGCTAAATTTCTCAACACCACAGTCAGTTAAGTCACCTACAGCCACCTTTGA
AAAACACGGAGAGCACCTACCCCGAGGAGAAGGTAGATTTGGAGTGAGCCGTCGCCGTCATAATTCTTCTGATGGCTTTT
TTAACAATGGACCCCTACGAACTACAGGAGATTCCTGGCACCAGCCCTCCCTATTCCGTCACGATTCTGTGGACTCTGGT
GTCTCTAAGGGAGCATATGCTGGAATCACAGGGAACCTGTCTGGTTGGCATGGTTCTTCCCGGGGTCATGATGGCATGAG
CCAGCGTAGCGGGGGTGGCACAGGGAACCATCGCCACTGGAATGGCAGCTTCCACTCCCGGAAAGGCGCTACCTTTCAGG
AAAAGCCATCTACAGAGATTAGGGAAGAAAAGAAAGAAGACAAGGTGGAAAAGTTGCAGTTTGAAGAAGAAGACTTTCCT
TCTTTGAATCCAGAAGCTGGCAAACAGAATCAGCCATGCAGACCTATTGGGATGCCTTCTGGAGTGTGGGAAAACCCACC
TAGTGCCAAGCAACCCTCCAAGATGCTGGTCATTAAAAAAGTTTCCAAAGAGGATCCTGCTGCTGCCTTCTCTGCTGCAT
TCACCTCACCAGGATCTCACCATGCAAATGGGAACAAATCATCAACCATAGTCCCAAGTGTCTATAAGAACCTGGTTCCT
AAGCCTGCACCACCACCTTCAAAGCCCAGTGCATGGAAAGCTAACAGAATGGAACACAAATCAGGGTCCCTTTCCTCTAG
CCGAGAGTCTACTTTTACCAGTCCGATCTCTGTTACCAAACCAGTGGTACTGGCTGGTGGCGCGGTTCTAAGCTCTCCCA
AAGAGAGTCCCTCCAGCACCACCCCTCCAGTTGAGATCACCTCCTCTCGTCTTACCAAGTTGACCCGCCGAACTACCGAC
AGGAAGAGTGAGTTCCTCAAGACTTTGAAGGATGACCAGAATGGAGACTTCTCAGAGAGCAGAGATTGTGACAAGCTGGA
GGATTTGGAGAATAGCACACCTGAACCAAAGGAAAATGAAGAAGAAGAATGTCATCAGAATGGCCTCGCTCTTCCTGTTG
TGGAGGAAGGGGAAGTCCTCTCTCACTCTCTGGAAGCAGAGCACAGGTTATTGAAAGCAATGGGATGGCAGGAATATCCT
GAAAATGATGAGAATTGCCTTCCCCTCACAGAGGATGAG

Alignment

ORF - retro_chof_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.34 %
• Parental protein coverage: 87.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQHDFVPAWLNFSTPQSVKSPTATFEKHGEHLPRGEGRFGVSRRRHNSSDGFFNNGPLRTTGDSWHQPS
          MAQHDFVPAWLNFSTPQSVKSPTATFEKHGEHLPRGEGRFGVSRRRHNSSDGFFNNGPLRTTGDSWHQPS
Retrocopy MAQHDFVPAWLNFSTPQSVKSPTATFEKHGEHLPRGEGRFGVSRRRHNSSDGFFNNGPLRTTGDSWHQPS

Parental  LFRHDSVDSGVSKGAYAGITGNLSGWH--SRGHDGMSQRSGGGTGNHRHWNGSFHSRKGSTFQEKPSTEI
          LFRHDSVDSGVSKGAYAGITGNLSGWH..SRGHDGMSQRSGGGTGNHRHWNGSFHSRKG.TFQEKPSTEI
Retrocopy LFRHDSVDSGVSKGAYAGITGNLSGWHGSSRGHDGMSQRSGGGTGNHRHWNGSFHSRKGATFQEKPSTEI

Parental  REEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGMPSGVWENPPSAKQPSKMLVIKKVSKEDPGAAL
          REEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGMPSGVWENPPSAKQPSKMLVIKKVSKEDP.AA.
Retrocopy REEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGMPSGVWENPPSAKQPSKMLVIKKVSKEDPAAAF

Parental  CAAFTSPGSHHGNGNKSSTMVPSVYKN-VPKPAPPVSKPSAWKANRMEHKSGSLSSSRESTFTSPISVTK
          .AAFTSPGSHH.NGNKSST.VPSVYKN.VPKPAPP.SKPSAWKANRMEHKSGSLSSSRESTFTSPISVTK
Retrocopy SAAFTSPGSHHANGNKSSTIVPSVYKNLVPKPAPPPSKPSAWKANRMEHKSGSLSSSRESTFTSPISVTK

Parental  PVVLAGGAVLSSPKESPSSTTPPIEITSSRLTKLTRRTTDRKSEFLKTLKDDQNGDFSESRDCDKLEDLE
          PVVLAGGAVLSSPKESPSSTTPP.EITSSRLTKLTRRTTDRKSEFLKTLKDDQNGDFSESRDCDKLEDLE
Retrocopy PVVLAGGAVLSSPKESPSSTTPPVEITSSRLTKLTRRTTDRKSEFLKTLKDDQNGDFSESRDCDKLEDLE

Parental  NSTPEPKENEEEECHQNGLALPVVEEGEVLSHSLEAEHRLLKAMGWQEYPENDENCLPLTEDE
          NSTPEPKENEEEECHQNGLALPVVEEGEVLSHSLEAEHRLLKAMGWQEYPENDENCLPLTEDE
Retrocopy NSTPEPKENEEEECHQNGLALPVVEEGEVLSHSLEAEHRLLKAMGWQEYPENDENCLPLTEDE

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_53 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53 ,
Microcebus murinus	ENSMICG00000008449	1 retrocopy	retro_mmur_164,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Mus musculus	ENSMUSG00000034042	2 retrocopies	retro_mmus_1391, retro_mmus_405,
Oryctolagus cuniculus	ENSOCUG00000017939	1 retrocopy	retro_ocun_427,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859,
Ochotona princeps	ENSOPRG00000001584	1 retrocopy	retro_opri_928,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Sorex araneus	ENSSARG00000004852	1 retrocopy	retro_sara_242,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243,
Tursiops truncatus	ENSTTRG00000012202	1 retrocopy	retro_ttru_1355,