RetrogeneDB ID: retro_chof_1121

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_205022:21..1498(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COIL
• Ensembl ID: ENSCHOG00000008740
• Aliases: None
• Description: coilin [Source:HGNC Symbol;Acc:2184]

Sequence

>retro_chof_1121
TTAGAAGAGAGAGGAGTTGCTGAGAATTCTGTAGTAGTCACTAATGGTGATGACACTCATTTATTACCTCGAAAAGCAAA
GAAGCGGGCGCTTAAGACTGAGGAGGAAGAAGCTGAACTAGATTACAGATATTCAAAGAAGCAATGGAAGAGGCAAGGGA
GCAATAACGAGAAGACCTTGGATCTGGAACCAAAAGTTGCCACAGGTCAGAGTGTGAGGAGAAAAAACAAGAAGAAAAAC
AAAATAATATGTGGTGGAATGGATGATGAGGAGGAGGAGGAGAAAAAAGGACAATCACCCAAGAAAAAGGAAAAATTTGA
ATATAAAAAACAGACAAAGAATCCCAAGTCTCCTAAAGCACAGACAGCGAAAGAGTGGACCATTCAGAACTGTAGTCCTC
CAAAAGGTTCTCCTGGAAAAAACAGCCTTGTTAAAGGTAAAAAGAAAGGTGGTGGAGGCATTTGTGAAAAAGACAGCCCC
AGTTCCTGCTCGGAGTCTGAGTCTTCTAATGAATCAACCCAGCAATGGACTCGGCAATGTCATTTTGGAGGTAAAAAGTC
TGAGAAAATATCAACTGAGCTGTCAAAGGAAGGATCCTGTCTGAAAAACCCACCTACAAACAAATTGGCTGCAAAAGCTG
GCTTTAACTTTACACCCATTAAGGGCAAGACAAGAAAAGCATCATCTTCTAGTTCAGACTCCAGTTCAGAGTCAGAAAAC
CAATGCATAATATCCAAGAGCACGGCGGTGTGTGCTGCAGGTTTCTTGAAAACAGCCGGCCTCTTTGCAGGGAGTGGTTG
TCCTGGGCCAGGGCCGTCCTCACAGACTCCAAGTGCTACCGGATGGAAGCACTCTGACTCGAATGGTGGCAGACAGGCTC
CTGGTCCTCCTCCCAACTTGTCTGTCCCCATCGGTTTGGGAAGAGGATGGGGTAGAGGAGAGGACCTTCTTTCTTGGAAG
GGAGCCAGGGGGCGGGGAGTACGGGGGAGAGGTCGAGGACGAGGGCAAACCATTCCTTGTGTTTTAAGCAGAAACAGCGA
CTATCAGAAGCAGCAACAATTAAATGAATTGCTAACAAACTCATCTACTATTATTCAGAATCCAGTAGAGATACAAAAGA
AGGACTATAGTCTGTTACCTCTATTAGCAGCTGCCCCTCAAGTTGGAGAAAAGATTGCATTTAAGCTTTTGGAACTAACA
TCCAATTACTCTCCTGATGTCTCTGAGTACAAGGAAGGAAAAATACTAAGCCATAATCCAGACACCCAGCAAGTAGATAT
AGAAATCCTTTCATCTTTACCTGCCATAAAAGAACCTGGGAAATTTGATTTGGTTTATCACAATGAAAATGGAACTGAGG
TAGTGGAGTATGCTGTCACACAGGAGAGGAAGATCACTGTTTTTTGGAGAGAATTGATTGACCCAAGATTGATTATTGAT
CCTCCCGAAAAATGACACATAAGATCCATCACTTGCT

Alignment

ORF - retro_chof_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.9 %
• Parental protein coverage: 85.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LEERGVAENSVVVTNGDDTHLLPRKAKKRALKSEEEEAELDYRYSKKQWKRQGSNSEKTLDLEPKVATGQ
          LEERGVAENSVVVTNGDDTHLLPRKAKKRALK.EEEEAELDYRYSKKQWKRQGSN.EKTLDLEPKVATGQ
Retrocopy LEERGVAENSVVVTNGDDTHLLPRKAKKRALKTEEEEAELDYRYSKKQWKRQGSNNEKTLDLEPKVATGQ

Parental  SVRRKNKKKNKIICGGMDDDEEEEKKGQSPKKKEKFEYKKQTKNPKSPKAQTAKEWTIQNCSPPKGSLGK
          SVRRKNKKKNKIICGGMDD.EEEE....................PKSPKAQTAKEWTIQNCSPPKGS.GK
Retrocopy SVRRKNKKKNKIICGGMDDEEEEEXXXXXXXXXXXXXXXXXXXXPKSPKAQTAKEWTIQNCSPPKGSPGK

Parental  NSLVKGKKKGGGGICEKDSPSSCSESESSNEST-SNGLGNVILEV-KKSEKISTELSKEGSCLKNPPTNK
          NSLVKGKKKGGGGICEKDSPSSCSESESSNEST.SNGLGNVILEV.KKSEKISTELSKEGSCLKNPPTNK
Retrocopy NSLVKGKKKGGGGICEKDSPSSCSESESSNEST>SNGLGNVILEV<KKSEKISTELSKEGSCLKNPPTNK

Parental  LAAKAGFNFTPIKGKTRKASSSSSDSSSESENQCIISKSTAVCAAGFLKTAGLFAGSGCPGPGPSSQTPS
          LAAKAGFNFTPIKGKTRKASSSSSDSSSESENQCIISKSTAVCAAGFLKTAGLFAGSGCPGPGPSSQTPS
Retrocopy LAAKAGFNFTPIKGKTRKASSSSSDSSSESENQCIISKSTAVCAAGFLKTAGLFAGSGCPGPGPSSQTPS

Parental  ATGWKHSDSNGGRQAPGPPPNLSVPIGLGRGWGRGEDLLSWKGARGRGVRGRGRGRGQTIPCVLNRNSDY
          ATGWKHSDSNGGRQAPGPPPNLSVPIGLGRGWGRGEDLLSWKGARGRGVRGRGRGRGQTIPCVL.RNSDY
Retrocopy ATGWKHSDSNGGRQAPGPPPNLSVPIGLGRGWGRGEDLLSWKGARGRGVRGRGRGRGQTIPCVLSRNSDY

Parental  QKQQQLNELLTNSSTIIQNPVEIQKKDYSLLPLLAAAPQVGEKIAFKXXXXXXXXXXXXXXXXEGKILSH
          QKQQQLNELLTNSSTIIQNPVEIQKKDYSLLPLLAAAPQVGEKIAFK................EGKILSH
Retrocopy QKQQQLNELLTNSSTIIQNPVEIQKKDYSLLPLLAAAPQVGEKIAFKLLELTSNYSPDVSEYKEGKILSH

Parental  NPDTQQVDIEILSSLPAIKEPGKFDLVYHNENGTEIVEYAVTQERKITVFWRELIDPRLIIDP-PNNNTS
          NPDTQQVDIEILSSLPAIKEPGKFDLVYHNENGTE.VEYAVTQERKITVFWRELIDPRLIIDP.P.N.T.
Retrocopy NPDTQQVDIEILSSLPAIKEPGKFDLVYHNENGTEVVEYAVTQERKITVFWRELIDPRLIIDP>PKNDT*

Parental  NASLA
          ..SLA
Retrocopy DPSLA

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_1121 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008740	1 retrocopy	retro_chof_1121 ,
Callithrix jacchus	ENSCJAG00000013960	1 retrocopy	retro_cjac_2240,
Dasypus novemcinctus	ENSDNOG00000023961	1 retrocopy	retro_dnov_1986,
Echinops telfairi	ENSETEG00000003687	1 retrocopy	retro_etel_1537,
Nomascus leucogenys	ENSNLEG00000008026	1 retrocopy	retro_nleu_1014,
Oryctolagus cuniculus	ENSOCUG00000011345	1 retrocopy	retro_ocun_1798,
Pongo abelii	ENSPPYG00000008248	1 retrocopy	retro_pabe_305,
Tupaia belangeri	ENSTBEG00000008882	4 retrocopies	retro_tbel_2118, retro_tbel_3549, retro_tbel_3961, retro_tbel_838,