RetrogeneDB ID: retro_chof_2540

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_83871:567..1815(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NCOA4
• Ensembl ID: ENSCHOG00000004343
• Aliases: None
• Description: nuclear receptor coactivator 4 [Source:HGNC Symbol;Acc:7671]

Sequence

>retro_chof_2540
CTATTGGGCCAGTTCAATTGTCTTATTCATCATCTGGAGCGCACCCAAAACAAAGAGCTAGCCAAGCAAGTCTCCGTGTG
TCTGGAGAGACTGGGCAGTTTGACAGTCAAACCCGAAGATTCCACTGTCCTGCTCTTTGACACAGATACAACTGCTCTGC
GCCAGACCATCACCATGTCTGGGTCCCTCAAGACCATCCAAATCCCTGAGCACCTGATGACTCATGCTGGTTCATCAAAT
ATCGGGCCCTTCCTGGAGAAAAGAGGTTATATTCCAGTGCCAGAACAGAAGTCATCATCCAGCACCACAGCTGTCCCCCT
TGGCGATTGGCTCCTCGGAAGCAAACCCACAAATGGTCACCAGGCTCCTCACGTGCCCAGCACCAACCCCCCAGACTGGC
TCTCCCCGCAGCAGACCTTGGAGAATAGTCAAACTGCCCCCAGAGCCTGCAATTTCAGTAATGTCTGGGGCAACCTAAAG
GGCTTGGAAAACTGGCTCAAGAGTCAGCAGCAAGAAGTTCCTGAAAAACCAAGTAACCAAAAGTGTAACAGCTATTCTAC
TGCCAGTTCTTTCTCCACTGAAGTTGAAAACGTCAGCAACCTAGAGCTTCTTGATGAAGATGAGACGGACCTTTCTGATT
GGCTGGTGACTCCCCAGGAACCCTGTAAGCTGGAGAAGCTGGAGAGTGGTAGCTGTGAAACCAGTGAGAAGTTTAAGCTC
TTGTTCCAGATTTTCCAGGAGTCCTATAGTGTGAGTGATTGGCTTGTCAAGCCTGACTCCTGTTCCAGTTGTCAGGGCAA
CCAGCCCAAAGGTGTGGAGATTGAAAACCTGGGCAATCTGAAGTGCCTGAATGACCACTTAGAGCCCAAGAAACTGCTAT
CCACCCCCAGCAAGATTACTGAGGATTGGCTTGTCCAGACACATCCAGAACCATATAAAGTAGAGGAGGTATGCAAAGCC
AATGAGCCCTGCACAAATTTTTCAGTATGTGCGTGTGATGAGAACTGTCAGAAGGAAGCTCTGTGTAAGTGGCTTCTGAA
GAAAGAAGGAATGGATAAAAATGGGATGCCAGTGGATCCAAAACCTGAGCCTGAGAAGCTTAAAGATTCCCTGAATATGC
AGCTCTGTCCTTCCAGAAAAGAGGCAACAAAACAGGCTAAGGCACCAAAGGCAATGGAACCTTTTAGAATTGCTGTTTCC
TTTCAAATCATAAGGAACAGTCCCTTGTCAGAATGGCTCATCAGATCT

Alignment

ORF - retro_chof_2540 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.22 %
• Parental protein coverage: 81.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLGQFNCLIHQLERTQIKELASQVSVCLERLGSLTLKPEDSTVLLFDADTTALRQTITTFGSLKTIQIPE
          LLGQFNCLIH.LERTQ.KELA.QVSVCLERLGSLT.KPEDSTVLLFD.DTTALRQTIT..GSLKTIQIPE
Retrocopy LLGQFNCLIHHLERTQNKELAKQVSVCLERLGSLTVKPEDSTVLLFDTDTTALRQTITMSGSLKTIQIPE

Parental  HLMTHAGSSNIGPFLEKRGYIPVPEQKSSSSTTAVPLGDWLLGSKPTNGHQAPHVPSTNPQDWLSPQQTL
          HLMTHAGSSNIGPFLEKRGYIPVPEQKSSSSTTAVPLGDWLLGSKPTNGHQAPHVPSTNP.DWLSPQQTL
Retrocopy HLMTHAGSSNIGPFLEKRGYIPVPEQKSSSSTTAVPLGDWLLGSKPTNGHQAPHVPSTNPPDWLSPQQTL

Parental  ENSQTAPRACNFSNVWGNLKGLENWL--LKSEKPSNQKCNSYSTASSFSTEVEKVSNLEHL---DEVEMD
          ENSQTAPRACNFSNVWGNLKGLENWL.....E.P...........S..S.....V.N...L...DE.E.D
Retrocopy ENSQTAPRACNFSNVWGNLKGLENWLKSQQQEVPEKPSNQKCNSYSTASSFSTEVENVSNLELLDEDETD

Parental  LSDWLVTPQEPCKLEKLESGSCETSEKFKLLFQIFQESYSVSDWLVKPDSCSSCQGNQPKGVEIENLGNL
          LSDWLVTPQEPCKLEKLESGSCETSEKFKLLFQIFQESYSVSDWLVKPDSCSSCQGNQPKGVEIENLGNL
Retrocopy LSDWLVTPQEPCKLEKLESGSCETSEKFKLLFQIFQESYSVSDWLVKPDSCSSCQGNQPKGVEIENLGNL

Parental  KCLNDHLEPKKPLSTPSKITEDWLVQTHPEPYKVEEVCKANEPCTSFSECVCDENCEKEALCKWLLKKEG
          KCLNDHLEPKK.LSTPSKITEDWLVQTHPEPYKVEEVCKANEPCT.FS.C.CDENC.KEALCKWLLKKEG
Retrocopy KCLNDHLEPKKLLSTPSKITEDWLVQTHPEPYKVEEVCKANEPCTNFSVCACDENCQKEALCKWLLKKEG

Parental  MDKNGMPVDPKPEPEKLKDSLNMWLCPSRKEATKHAKAPKAMEPFRIADSFQIIRNSPLSEWLIRS
          MDKNGMPVDPKPEPEKLKDSLNM.LCPSRKEATK.AKAPKAMEPFRIA.SFQIIRNSPLSEWLIRS
Retrocopy MDKNGMPVDPKPEPEKLKDSLNMQLCPSRKEATKQAKAPKAMEPFRIAVSFQIIRNSPLSEWLIRS

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_2540 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019565	1 retrocopy	retro_btau_1761,
Choloepus hoffmanni	ENSCHOG00000004343	1 retrocopy	retro_chof_2540 ,
Callithrix jacchus	ENSCJAG00000013352	1 retrocopy	retro_cjac_916,
Myotis lucifugus	ENSMLUG00000000619	1 retrocopy	retro_mluc_2161,
Mus musculus	ENSMUSG00000056234	1 retrocopy	retro_mmus_14,