RetrogeneDB ID: retro_chof_1161

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_215378:602..1335(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000006159
• Aliases: None
• Description: None

Sequence

>retro_chof_1161
GGGATCCTGGATCTAGGAATTAAAGATCTCATTGTGCTATATTGCCAGATTTTCTTACTGTTTGCTCTTCTTACTTTAAT
CACATCTGTGACTACCTCATTGATGAACTCATTTAAATGTTCCTAAGTTTTCTGAAAGAAGAAGGAACGAATGAGAAAAG
GCAAAAGCTTGTGCAAAACAAAGAAGAGGCACAGAGTGAAAAGGCCAGCAGATACAGAGAAGTTTTGAAACCTTACTAGG
AAATGAAATTTAAAAAAACTGGAAAAGTGCTTTCATCAGATGATGGGTGAAACCTGGAAGTTAAGCGATGGTCACAAACT
TGGGGGTGATGAGTTGGTACTTGAAAGTGCCAGCCAGACATCTTCTGAAACTTCAAGCAGAGAAGCTGCAGAGACAAAAT
TTGCCTAAGCCTGTAACCAAACTTTCACGACCTCCTGAACAGCCCACACAGAAGAAGTTTCTTGATTTACCTGAAGAAAC
TCCTAAAACAGACAAAGAAGTAGTTACTGTTGCTCTCAGATATCCAACTGGCAGTGTCCTGAAGAGAAGGTTTTTGAAGT
CTTACAGTTCACAGGTCTCATTTGATTGACTGGTGAAAACTCGTTACTTCACATCCCCAGATAGCCTTTCTACTTCCTTT
CCCAGAAGACCTCTGGAATTGGACAGAGGTTGGTCATTGGAAGACATAGGAATAACTGTGGATACAGTACTCAGTGTGGA
AGAGAAAGAGCGA

Alignment

ORF - retro_chof_1161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.68 %
• Parental protein coverage: 90.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GIPDLGIKDLVLLCGRIFLLLALLTLIISVTTSWLNSFKSSQV-YLKEEEEEKNGKRQKLVLNRQQETQS
          GI.DLGIKDL..L...IFLL.ALLTLI.SVTTS..NSFK.S.V..LKEE....N.KRQKLV.N...E.QS
Retrocopy GILDLGIKDLIVLYCQIFLLFALLTLITSVTTSLMNSFKCS*V<FLKEEGT--NEKRQKLVQNKE-EAQS

Parental  EKASRYIEKVLKPHQEMK-LKKLEERFYQMSGETWKLSNGHKLGGDEGLVLENASQTSETSNREAA-RRR
          EKASRY.E.VLKP..EMK.LKKLE..F.QM.GETWKLS.GHKLGGDE.LVLE.ASQTS.......A..R.
Retrocopy EKASRYRE-VLKPY*EMK>LKKLEKCFHQMMGETWKLSDGHKLGGDE-LVLESASQTSSETSSREA>QRQ

Parental  NLPEPVTKLSRPPDQPT-KKXXXXXXXXXXXXXXVVTVALRCPSGSMLK-RRFKTCXXXV-LDWMMKIGY
          NLP.PVTKLSRPP.QPT.KK..............VVTVALR.P.GS.LK.R..K.....V..D...K..Y
Retrocopy NLPKPVTKLSRPPEQPTQKKFLDLPEETPKTDKEVVTVALRYPTGSVLKRRFLKSYSSQVSFD*LVKTRY

Parental  HTSLYSLSTSFPRRPLEVEGGWSLEDIGITVDTVLNVEEKEQ
          .TS..SLSTSFPRRPLE...GWSLEDIGITVDTVL.VEEKE.
Retrocopy FTSPDSLSTSFPRRPLELDRGWSLEDIGITVDTVLSVEEKER

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_1161 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001600	2 retrocopies	retro_amel_1272, retro_amel_1326,
Choloepus hoffmanni	ENSCHOG00000006159	4 retrocopies	retro_chof_1161 , retro_chof_1175, retro_chof_1383, retro_chof_1500,
Myotis lucifugus	ENSMLUG00000016846	1 retrocopy	retro_mluc_606,