RetrogeneDB ID: retro_chof_1924

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_42405:9647..11005(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPR128
• Ensembl ID: ENSCHOG00000009379
• Aliases: None
• Description: G protein-coupled receptor 128 [Source:HGNC Symbol;Acc:19241]

Sequence

>retro_chof_1924
AACACTAAGGCATTTGGCTTTGTAGTGTTTCAAAACAACAAGCTTTTCCAATCAAAAACTTTCACAACTAAATCAAATTT
TAGTCAAAGAATTATCTCAAGCAGCATTGAGACAAATGCTTCTGGTAAGAGTTCTTCTGTTGAAATGGTCTTTAATCCAA
AGCACAACCAATTGCAATTTGATCTCCATTCCTTTGCCTGTGTCTTTTGGAATTTTTCAAAGAAGGATTGAAGCACAAAT
GGCTGTCTCAAAGAGAGGCGCACTGATGGATTCCTGCACTGCCACTATAATAATGCCACTAACTTTGCTGTATTAATGCA
TTTCAGAAAGAAATATCAATATCCTGAATCACTAGACATATTATCAACTGTTGGTTGTGCACTGTCCATTGCTGGTCTGG
CTCTCATGATTATATTTCAGGAAAATCAGAAAAACTTCAGTAACCTGGGTGTTGGTTGGTCTGTGCACATCGATGTTGAT
TTTCAACCTCCTCTTTGTGTTCGGAATTGAAAACTCCAATAAGAACTTAAAGATGAGTGACATCAGTACCAACAATACTG
GCACTGACAATGATGAGATCCCCACAACAGACACTAACAGCCCGAATGCCACATGCACTGTGATGGCAGCCTTACTGCAC
TATTTTCTGTTAGCGACATTTACCTGGACTGGGCTCAGTGCTGCACAGCTCTATTTCCTTCTAATTAGGACCATGAAACC
CCTTCCAACACATTTCATTCTCTTCATATCTTTAATTGGATGGAGCTTCCTGGATATAGTGGTGGCTTTATCAGTGGGAA
TTCTTTATTCTCAGAATGGGAGCAATTCACAGCTGGGGTTAGACTACCGACAAGAGGAGATCTGCTGGCTGGCAGTTCCA
GAAAGCAATGTTTTTATAACAAGTCCATGTTTGTGGTCATTCATCATACCTGTGACCATCATCCTAATCAGCAATGTTGT
TATATTTGTTGTCATCACAGTCAAAGTGTTGTGGAAGAATAACCAGAATCTGACAAGCCCCAAAAAAGTTTTCATCCATG
AAGAAAGTCCTTAGTACATTATCTATTGCAGTCATTTTTGAAATTAGCTGGATTCTGGCATTCCTTATGGTAGTTGCTAA
TGGTGATATCAGGATCATCTTAAACTACATATTCTGCCTTTTCAGTACTACCCAGGGATTGCAAATTTTTATCCTTTACA
CTGTTAGAACAGAAATCTTTCAGAGCGAGGCTTCCAAAGTGTTGAAGTCCCTCTTGTCATCTGCTGGGAGACTGAAGTCA
ATACCATCGTTCACTCAACCAAAGCTGCGTATCAGGATGTATAATATGCTCAGATCCTTTCCAACCCTAAGTGAACAC

Alignment

ORF - retro_chof_1924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.38 %
• Parental protein coverage: 57.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DTTACGFVMFQNNKLFQSKIFRPRSNFNHRVISRSIETSDSEKRASVEMVFNPKHNQKQFDLHSYACVFW
          .T.A.GFV.FQNNKLFQSK.F...SNF..R.IS.SIET..S.K..SVEMVFNPKHNQ.QFDLHS.ACVFW
Retrocopy NTKAFGFVVFQNNKLFQSKTFTTKSNFSQRIISSSIETNASGKSSSVEMVFNPKHNQLQFDLHSFACVFW

Parental  NVTKEDWSTVGCFKERRTDGFLHCHCNHTTNFAVLVSFRKIYKYPASLDVLSTVGCALSIAGLALTIIFQ
          N..K.D.ST.GC.KERRTDGFLHCH.N..TNFAVL..FRK.Y.YP.SLD.LSTVGCALSIAGLAL.IIFQ
Retrocopy NFSKKD*STNGCLKERRTDGFLHCHYNNATNFAVLMHFRKKYQYPESLDILSTVGCALSIAGLALMIIFQ

Parental  IVTRKVRKTSVTW-VLVSLCTSMLIFNLLFVLGIENSNKNLKMSDINTNNTGTDNDEIPTTDIVNTPNPM
          ..........V.W....S.....L.F...F.....N.N..LKMSDI.TNNTGTDNDEIPTTD..N.PN..
Retrocopy ENQKNFSNLGVGW>LCTSMLIFNLLF--VFGIENSNKN--LKMSDISTNNTGTDNDEIPTTD-TNSPNAT

Parental  CTVMAALLHYFLLATFTWTGLSAAQLYFLLIRTMKPLPPHFILFISVIGWGVPAIVVSLTVGILYSQNGS
          CTVMAALLHYFLLATFTWTGLSAAQLYFLLIRTMKPLP.HFILFIS.IGW....IVV.L.VGILYSQNGS
Retrocopy CTVMAALLHYFLLATFTWTGLSAAQLYFLLIRTMKPLPTHFILFISLIGWSFLDIVVALSVGILYSQNGS

Parental  NSQWELDYRQEEICWLAVPESNGFITSPFLWSFIIPVAIILISNVVIFVIITVKVLWKNNQNLTSTKKV-
          NSQ..LDYRQEEICWLAVPESN.FITSP.LWSFIIPV.IILISNVVIFV.ITVKVLWKNNQNLTS.KKV.
Retrocopy NSQLGLDYRQEEICWLAVPESNVFITSPCLWSFIIPVTIILISNVVIFVVITVKVLWKNNQNLTSPKKV>

Parental  SSIKKILSTLSIAVIFGITWILAFLMLVDNDDIRIILSYVFCLFNTTQGLQIFILYTVRTGIFQREASKV
          SS.KK.LSTLSIAVIF.I.WILAFLM.V.N.DIRIIL.Y.FCLF.TTQGLQIFILYTVRT.IFQ.EASKV
Retrocopy SSMKKVLSTLSIAVIFEISWILAFLMVVANGDIRIILNYIFCLFSTTQGLQIFILYTVRTEIFQSEASKV

Parental  MKSLSSSAERVKSVPLFRKPKLRVRMYNMIRSFPTPKEH
          .KSL.SSA.R.KS.P.F..PKLR.RMYNM.RSFPT..EH
Retrocopy LKSLLSSAGRLKSIPSFTQPKLRIRMYNMLRSFPTLSEH

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_1924 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009379	1 retrocopy	retro_chof_1924 ,