RetrogeneDB ID: retro_chof_325

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7351:67227..68015(-)
• Located in intron of: ENSCHOG00000001647

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_325
TTCAAGACAATGAGAGGGGGGCCAGTATGAAAGAAACATTGTATCACCTACAGAAGCAACAACTACACTACTGACTTGGT
GCATGCAGATGTCGACTATGCCAGCCAGAAGGCTTTTCAAGTATGGAGTGATGTGACATACCACCGCCCCCCCTTGAAAT
TCATAAACATTAATACAGGTGAGGCTGACATTATGATCTCTTCTTCATGTGGAGCTCAGGGAGTCCTCTACCCTTTTGAT
GGAAAAAGTGGCGTTTTAGCCCACGCTTTTGGACCTGGAGCTGGTATTGGAGAAGATGCACATTTTGATGAGGATGAAAT
CTGGACTAAAAATTCCAGAGGTCTAAACTTATTTCTTGTTGTGGTTCATGAGATTTGCCATTCCTTGGGTCCTAACCATT
CCAATGAACCAAGGGTCGTATGTTCCCCACCTACAGTTATGTTGACCCCAACACATTTAGCCTCTCTACTGTTAACATAC
ACGTCACTCAGTTCCTCTACAGAGGCCCAGAACAGCACCAACCCAAGCCAGATCCCTAATCTGTCTATCTGTGGCCCTAA
TTTGAGGTTCGATGCTGTCATTATAGTCGAAAATATAATCTTTTTCCTTAAAAACAGGTTCTTCTGGTGGAAGCATGCTG
AGACACCTAAGATCAGTGTTAGTTTAATTCTAACTTATGGCCAACTTTGCTATCTGGTATCCAAGCTGCCTACGAAATTG
GAGCCAGAAATGAAGTTTTTCTTTTTAAAGATGACAAGTACTGGTAAATCAGCAATTTAAGAACACAC

Alignment

ORF - retro_chof_325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.06 %
• Parental protein coverage: 55.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FKTMRGGPVWKKHFITYRINNYTTDLARADVDDAIQKAFQVWSDVT----PLKFRRISAGEADIMILFSR
          FKTMRGGPV.KKH.ITYR.NNYTTDL..ADVD.A.QKAFQVWSDVT....PLKF..I..GEADIMI..S.
Retrocopy FKTMRGGPV*KKHCITYRSNNYTTDLVHADVDYASQKAFQVWSDVTYHRPPLKFININTGEADIMISSSC

Parental  REHGDFYPFDGKNGILAHAFGPGAGIGGDAHFDDDEIWTKNSRGHNFFLVAVHEIGHSLGLDHSNDPKAI
          ...G..YPFDGK.G.LAHAFGPGAGIG.DAHFD.DEIWTKNSRG.N.FLV.VHEI.HSLG..HSN.P...
Retrocopy GAQGVLYPFDGKSGVLAHAFGPGAGIGEDAHFDEDEIWTKNSRGLNLFLVVVHEICHSLGPNHSNEPRVV

Parental  -MFPTYRYVDLHTFSLSSDDIRGIQFLYGGPEQHQPKP-VPDEDVCDPNLRFNAVTTVGNKIFFFKDRFF
          .MFPTY.YVD..TFSLS...I...QFLY.GPEQHQPKP..P....C.PNLRF.AV..V.N.IFF.K.RFF
Retrocopy <MFPTYSYVDPNTFSLSTVNIHVTQFLYRGPEQHQPKP>IPNLSICGPNLRFDAVIIVENIIFFLKNRFF

Parental  WWKHVETPKISISSI-SNLWPTLPSGIQAAYEIGARNEVFLFKDDKYWLISNLRIH
          WWKH.ETPKIS.S.I.SNLWPTL.SGIQAAYEIGARNEVFLFKDDKYW.ISNLR.H
Retrocopy WWKHAETPKISVSLI<SNLWPTLLSGIQAAYEIGARNEVFLFKDDKYW*ISNLRTH

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_325 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,