RetrogeneDB ID: retro_chof_601

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_125631:2660..3347(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNA12
• Ensembl ID: ENSCHOG00000003770
• Aliases: None
• Description: guanine nucleotide binding protein (G protein) alpha 12 [Source:HGNC Symbol;Acc:4380]

Sequence

>retro_chof_601
AGACACCATCTTCACAACATCCTCAAGGGCTCCCAAGTCCTTGTTGATGCCAAGACAAGCTTTGTATTCCTTGGCAGGAT
TCTGAAAATGAAAAAGCACAGGATGTTCTTAAAGGCCTTCCAGAACAAAACAGGCCTGCTTGTGGAGCCTGCCACCTTCC
AGCTGTTGTACCTGCTTTGAGGCTCCCTGGAAGGATTCTGGCATCAAGGAAGCATTCAGCCTGAGGAGTGAGTTCCAGCT
GGGTGAATCACTGAGGTATTCCTGGAAAACTTGGAGTGCATTGGCCAACTGAATTACTTTCCTAGTAAGCAAGACATCCT
GCTGGCTAAGAAAGCCACCAAGGGAATTGTGGAACATGATTTCAAGATGAATAAAATCCCTTTTATAATGGTGAATATGG
GCAGTCACCAGTCTCAGGGCCAGAAGAGTTTCCAGTGTTTTGAAAGAACCATGTCCATCCTGTTCATGGTGTTCTCCACA
GAGAGGACCAGGTCCTCATGGAGGACAGTGCACCAACCGGCTGGAAGAGTTGATCAACATCTTTGAGGTTGTAGTCAACA
ACAAGCTCTTCTTCAGCATCTCCTTAATTCTGTTCCTAGCACGATGGACATCCTGGTGGAGAAGGTGAAGATGGTCAGCA
TCAGGAAGCACTTCCCGCATTTCAAGGATGACTCTTACAGTCTGAAG

Alignment

ORF - retro_chof_601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.46 %
• Parental protein coverage: 61.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  RDTIVNILKGSRVLVDAR-DKLGIPWQYSENEK-HGMFLMAFENKAGLPVEPATFQLY-VPAL-SALWRD
          R....NILKGS.VLVDA..DKL.IPWQ.SENEK.H.MFL.AF.NK.GL.VEPATFQL..VPAL..A.W.D
Retrocopy RHHLHNILKGSQVLVDAK<DKLCIPWQDSENEK>HRMFLKAFQNKTGLLVEPATFQLL<VPAL<EAPWKD

Parental  SGIREAFSRRSEFQLGESVKY-FLDNLDRIGQLNYFPSKQDILLARKATKGIVEHDFVIKKIPFKMVDVG
          SGI.EAFS.RSEFQLGES..Y.FL.NL..IGQLNYFPSKQDILLA.KATKGIVEHDF...KIPF.MV..G
Retrocopy SGIKEAFSLRSEFQLGESLRY<FLENLECIGQLNYFPSKQDILLAKKATKGIVEHDFKMNKIPFIMVNMG

Parental  GQRSQRQKWFQCFDGITSILFMVSSSE-YDQVLMED-RRTNRLVESMNIFETIVNNKLFFNVSIILFL-N
          ...SQ.QK.FQCF....SILFMV.S.E..DQVLMED...TNRL.E..NIFE..VNNKLFF..S.ILFL..
Retrocopy SHQSQGQKSFQCFERTMSILFMVFSTE<EDQVLMED<QCTNRLEELINIFEVVVNNKLFFSISLILFL<S

Parental  KMDLLVEKVKTVSIKKHFPDFRGDPHRLE
          .MD.LVEKVK.VSI.KHFP.F..D...L.
Retrocopy TMDILVEKVKMVSIRKHFPHFKDDSYSLK

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_601 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003770	4 retrocopies	retro_chof_1344, retro_chof_2083, retro_chof_601 , retro_chof_653,
Choloepus hoffmanni	ENSCHOG00000012718	1 retrocopy	retro_chof_359,
Tursiops truncatus	ENSTTRG00000003798	1 retrocopy	retro_ttru_840,