RetrogeneDB ID: retro_chof_1900

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_41862:6056..7065(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC17
• Ensembl ID: ENSCHOG00000013916
• Aliases: None
• Description: leucine rich repeat containing 17 [Source:HGNC Symbol;Acc:16895]

Sequence

>retro_chof_1900
GAAAACAATATGCTTTCCATGTTTAAAAAGCTGAAAAACCTGGATCTGCAACAGAATGAGATCTCCAAAATTGAAAGTGA
GGCTTTCTTTGTTTTAAGCAAACTCGCCACCCTCTTACTGCAGCACAACCAGATCAAAGTCTTGATGGAAGAGCTGTTCA
TTTCTACATCTCTCCTGAGCTACCTGCGTCTTTATGACAACCCTTGGCACTGTACATGTGAGATCGAAATGCTCATCTCA
ATGCTGCAGATTCCAAGGAATTGGAATTTGGAGAACTATGCCAAATGTGAAAACCCACAAGAACTAAAGAATTAAAAAAC
TGTGGCAGATAAAACCTAAACAGTTATGCAGTGAAGGAGAAAAGGAACAATTAGACTCCAAACCCAAAGTACGAGGGAGA
CCCCCAGTCACCAAGCCTGGGGTGGCCTCTACTGTTTGCCACAATTATGTGTTTCCATACAAATGCTGGACTGCAAAAAA
AAAAAAAAGTTGGAGAAAGTTCCAAACAACATCCCTCCAGATATTATTAAACTTGACTTATCACACAGTAAGATCAACCA
GCTTTGACCCAAGGAATTTGAAGGTGTTCATGAGCTAGAGAAATTAAATCTCAGTAGCAATGGCATTGAATTCATAGATC
CTGCTGCTTTCTCAGGGCTTACTCACTTTGAAGAGTTAGATTTATCAAACAACAGTCTGCAGAACTTTGAACATGGAATA
TTAGAAGACTTGTATTTTTTGAAACGTTTTTGGCTCAGAGATAACCCTTGGAGATGTGACTACAACATCCACTACCTCTA
TTACTGGTTAAAGCACCACTACAATATCCACAATAACAGCCTGGAATGCAAAGTGCCTGAAGAATGCAAAGGGTGGTTTG
TGGGGAGATATGTTCAGAGTTACTTTGAAGAATGTGGCAAAGACAAGTTACCAGCATACCCTGAAACATCTGACCAGGAT
ACTGAAGATGACTAATAGGAAAAAAATACATAGGGATCATATAACAAAG

Alignment

ORF - retro_chof_1900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.94 %
• Parental protein coverage: 77.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KNNMFSKFKKLKSLDLQQNEISKIESEAFFGLSKLTTLLLQHNQI-VLTEEMFIYTTLLSYLLLCDNPWH
          .NNM.S.FKKLK.LDLQQNEISKIESEAFF.LSKL.TLLLQHNQI.VL.EE.FI.T.LLSYL.L.DNPWH
Retrocopy ENNMLSMFKKLKNLDLQQNEISKIESEAFFVLSKLATLLLQHNQIKVLMEELFISTSLLSYLRLYDNPWH

Parental  C--EIEMLISVLQIPRNQNLGNYAKCKSPQELKN-KKLLQIKSEQLCNEGEKEQLDPKPQVSGRPPVIKP
          C..EIEMLIS.LQIPRN.NL.NYAKC..PQELKN.KKL.QIK..QLC.EGEKEQLD.KP.V.GRPPV.KP
Retrocopy CTCEIEMLISMLQIPRNWNLENYAKCENPQELKN>KKLWQIKPKQLCSEGEKEQLDSKPKVRGRPPVTKP

Parental  EVDSTLCHNYVFP-IQTLDCKREX-LKKVPKNIPPDIVKLDLSYNKINQLRPKEFEDVHELRKLNLSSNG
          .V.ST.CHNYVFP.IQ.LDC...X.L.KVP.NIPPDI.KLDLS..KINQL.PKEFE.VHEL.KLNLSSNG
Retrocopy GVASTVCHNYVFP<IQMLDCXXXXXLEKVPNNIPPDIIKLDLSHSKINQL*PKEFEGVHELEKLNLSSNG

Parental  IEFIDPAAFSGLTHLEELDLSNNSLQNFDYGVLEDLYFLKLLWLRDNPWRCDYNIHYLYYWLKHHYNVHY
          IEFIDPAAFSGLTH.EELDLSNNSLQNF..G.LEDLYFLK..WLRDNPWRCDYNIHYLYYWLKHHYN.H.
Retrocopy IEFIDPAAFSGLTHFEELDLSNNSLQNFEHGILEDLYFLKRFWLRDNPWRCDYNIHYLYYWLKHHYNIHN

Parental  NGLECKIPEEYKGWFVGKYVRSYFEECPKDKVPAYPETFDQDTEDD-EWEKIHRDHVAK
          N.LECK.PEE.KGWFVG.YV.SYFEEC.KDK.PAYPET.DQDTEDD....KIHRDH..K
Retrocopy NSLECKVPEECKGWFVGRYVQSYFEECGKDKLPAYPETSDQDTEDD>NRKKIHRDHITK

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_1900 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013916	1 retrocopy	retro_chof_1900 ,
Felis catus	ENSFCAG00000009938	1 retrocopy	retro_fcat_470,