RetrogeneDB ID: retro_chof_106

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_2108:43271..43720(-)
• Located in intron of: ENSCHOG00000011192

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000010216
• Aliases: None
• Description: None

Sequence

>retro_chof_106
GAAAGAAGTCACAGGATAACTAAGCAGATTGTCACTGGCACCTCTGGCACTGTCCTGGACTGGTTATAAAAGGTCAAGCT
CATCAACTTCAAGATCAAAGTGTTTGCTGTGGATGAGGTTGACTTGTTGATAGTTACCCAGGGCCAAGATCACAGCATCC
ACATCCAGATGATGCTGCCCAGGAATGGCCAAATACTGTTTTTCTCTGTTACCGTTGGAGACTTTGCTTGGAAATTCACC
CAGAAAATGGTCCCAGACCTGTATATTTAATCAAACTGCAGCATGAGGAAAAGACCTTGGATACCATCAAGGAGTATTGT
ATCCTTGCAACAACAGAATTTTGAGCCTTGTTTAACCTCTTTGAGGCCATCCCCATTGCTCAAGCTATGATCTTCTGCCA
TACATGCGAAACAGCTAATTAGCTGGCAGCAGAGCTCTCAAAAGAAGGT

Alignment

ORF - retro_chof_106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 55.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERGQKITEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLF
          ER...IT.QIV.GT.GTVLDW..K.K.I...KIKVF..DE.D..I.TQG.QD.SI.IQ.MLPRN.Q.L.F
Retrocopy ERSHRITKQIVTGTSGTVLDWL*KVKLIN-FKIKVFAVDEVDLLIVTQG-QDHSIHIQMMLPRNGQILFF

Parental  SATFEDSVWKFAQKVV-PDP-NIIKLKREEETLDTIKQYYVLCNNRDEKFQALCNLYGAITIAQAMIFCH
          S.T..D..WKF.QK.V.P.P...IKL..EE.TLDTIK.Y..L.......F.AL.NL..AI.IAQAMIFCH
Retrocopy SVTVGDFAWKFTQKMV<PRPVYLIKLQHEEKTLDTIKEYCILATT---EF*ALFNLFEAIPIAQAMIFCH

Parental  TRKTASWLAAELSKEG
          T..TA..LAAELSKEG
Retrocopy TCETAN*LAAELSKEG

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_106 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010216	1 retrocopy	retro_chof_106 ,
Sus scrofa	ENSSSCG00000002722	1 retrocopy	retro_sscr_1023,
Ictidomys tridecemlineatus	ENSSTOG00000025733	1 retrocopy	retro_itri_1877,
Tupaia belangeri	ENSTBEG00000009816	1 retrocopy	retro_tbel_3669,