RetrogeneDB ID: retro_chof_2207

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_58255:3300..4019(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000008413
• Aliases: None
• Description: None

Sequence

>retro_chof_2207
CTGGAATTCAGAAAACTTAATGCAGGCGAGGCTGACAGTATAATGTCTTTTTCACATGGAGATCATGGAGATTTATGTTG
TTTTGATGGAAGAAGTAGAATTTTAACCCATGCTTTTGCACCTGGAGTTGCTGCTGGAGGAAATGCACATTTTGATGAGG
ATGAAATCTGGGCTAAAACCACCAGAGACATCAATTTCTTTCTTGCTGCTATTCATGAGATTGGCCGTTCCTTGGGTCTT
GACCATTCCAATGATTCAAGGCCACAATGTTTCCCACCTACGGTTATGTTGACCCCAACACATTTCGCCTCTCTACTGAT
GACATACATGGCATTCAGACCCCCTGTGGAGGCCCAGAAGAGCACCAATCTATGCCAGTTCCCAATAGTGCAGAACTTGT
GTATATCTGAGACCTCAATTCGAGGTTCAATGCTGTCACTACAATCAGAAACAAAATATTTTTCTTGAAAGACAGGTTCT
TTTGGTGGAAGCATCCTGAGATACCTAAGATCAGTGTTAGTTTAATTTCTAACTTATGACCAACTTTGCCATCTGGTATT
CAAGCTACTTATGAAATTGGAGCCAGAAATGAAGTTTTTCATTTTAAAGATGGCAAGTACTGGTTAATCAGCAATTTAAG
ACCACAACCAAACTATCTGAAGAGCATACATTCTTTGGGTTTCCCTGACTCTGTGAAAAAAAAACAATTCAGTTATTTT

Alignment

ORF - retro_chof_2207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.56 %
• Parental protein coverage: 50.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKFRRISAGEADIMILFSRREHGDFYPFDGKNGILAHAFGPGAGIGGDAHFDDDEIWTKNSRGHNFFLVA
          L.FR...AGEAD....FS...HGD...FDG...IL.HAF.PG...GG.AHFD.DEIW.K..R..NFFL.A
Retrocopy LEFRKLNAGEADSIMSFSHGDHGDLCCFDGRSRILTHAFAPGVAAGGNAHFDEDEIWAKTTRDINFFLAA

Parental  VHEIGHSLGLDHSNDP-KAIMFPTYRYVDLHTFSLSSDDIRGIQFLYGGPE--QHQPKPVPDEDVC--DP
          .HEIG.SLGLDHSND..KA.MFPTY.YVD..TF.LS.DDI.GIQ...GGPE..Q..P.P...E.V...D.
Retrocopy IHEIGRSLGLDHSNDS<KATMFPTYGYVDPNTFRLSTDDIHGIQTPCGGPEEHQSMPVPNSAELVYI*DL

Parental  NLRFNAVTTVGNKIFFFKDRFFWWKHVETPKISISSISNLWPTLPSGIQAAYEIGARNEVFLFKDDKYWL
          N.RFNAVTT..NKIFF.KDRFFWWKH.E.PKIS.S.ISNL.PTLPSGIQA.YEIGARNEVF.FKD.KYWL
Retrocopy NSRFNAVTTIRNKIFFLKDRFFWWKHPEIPKISVSLISNL*PTLPSGIQATYEIGARNEVFHFKDGKYWL

Parental  ISNLRIHPDYPKSIYSLGLPASVKKIDAAVF
          ISNLR..P.Y.KSI.SLG.P.SV.......F
Retrocopy ISNLRPQPNYLKSIHSLGFPDSVXXXQFSYF

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_2207 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008413	6 retrocopies	retro_chof_1424, retro_chof_1611, retro_chof_2207 , retro_chof_325, retro_chof_595, retro_chof_645,
Equus caballus	ENSECAG00000019445	1 retrocopy	retro_ecab_153,
Loxodonta africana	ENSLAFG00000010062	1 retrocopy	retro_lafr_147,
Macaca mulatta	ENSMMUG00000004250	1 retrocopy	retro_mmul_2325,
Otolemur garnettii	ENSOGAG00000010221	1 retrocopy	retro_ogar_965,