RetrogeneDB ID: retro_chof_653

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_131597:9..942(+)
• 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_653
AGCAGCAAGCCCACCTTCCTCAAGCAGATGGGCAACATCCACAGCCGCGAGTTTGACAGGAAGGCGCTGCTCGAGTTCCC
AGACACCATCTTTGACAACATCATTAAGGGCTCCAGAGTCCTTGTTGATGCCAAGACAAGCTTGGTATTCCTTGGCAAGT
TTCTGAAAATGAAAGTACGGAACATTCTTAATGGCCTTTGACAAGGAACAGGACTGCCCCTGGAGCCTCCACTTTCCAGC
TGTTGCACCTGCTTTGAGCACTCCCTGGAGGGATTCTGGCATCAGGGAAGGGTTCAGCCTGAGGAGTGAGTTCCAGCTGG
GTGGATCATTGAAGTACTGCTGGAAAACTTGGACTACATTGGCCAGATGAATTACTTTCCCAGTAAGCAAGACATCCTGC
TGTCTAGGAAAACCACCAAAGGAATTGTGAAACAGGATCTCATGATCAGAAAATCCCTTTTAAGTTGATGGATGTGGGTG
GCAAGTGGTCTTGGCACCAGAAGTGGTTCCAGTGTTTTGACGGGATCATGTACATCCTGTTCATGGTGTCCTCTAATTAG
AGGACTAGGTTTTCATGGAGGATAGGTGCACCAACTGGCTAGTGGAGTCAGGAATATTTTTGAAACCATAGTCAACAGCA
AGCTCTTCTTCAACGTCTCCATCATTCTGTTCCTCAGCAAGTTGGAACTCCTGATCGAAAAGGTGAAGATGGTCAGCATC
AAGAAGCACTTCCCAGATTTCAAGGGTGATACCCACAAGTTGGATGATGGGCAGTGCTACCTAGTCCAGTGTTCTGAAAG
AAAAGGATGAAACTGCAGTAAGCCACTCTTCCACCATTTTGTTACTGCCATCAACAGGGAGAACATCTACTTCATGTTTC
AAACTGTGAAGGACACAATCTTGCAAGAAAATCTGAAAGATATTATGTTCCAG

Alignment

ORF - retro_chof_653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.21 %
• Parental protein coverage: 83.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  SSKFTFLKPMYLIHACKFNL-ALLEFRDTIV-NILKGSRVLVDAR-DKLGIPWQYSENE-KHGMFLMAFE
          SSK.TFLK.M..IH...F...ALLEF.DTI..NI.KGSRVLVDA..DKLGIPWQ.SENE.K.G.FLMAF.
Retrocopy SSKPTFLKQMGNIHSREFDRKALLEFPDTIFDNIIKGSRVLVDAK<DKLGIPWQVSENE<KYGTFLMAFD

Parental  NK-AGLPVEP-ATFQLY-VPALSALWRDSGIREAFSRRSEFQLGESVKY-FLDNLDRIGQLNYFPSKQDI
          ....GLP.EP..TFQL...PALS..WRDSGIRE.FS.RSEFQLG.S.KY..L.NLD.IGQ.NYFPSKQDI
Retrocopy KE<TGLPLEP<STFQLL<APALSTPWRDSGIREGFSLRSEFQLGGSLKY<LLENLDYIGQMNYFPSKQDI

Parental  LLARKATKGIVEHDFVIKK-IPFKMVDVGGQRSQRQKWFQCFDGITSILFMVSSS-EYDQVLMEDRRTNR
          LL.RK.TKGIV..D..I.K.IPFK..DVGG..S..QKWFQCFDGI..ILFMVSS....D.V.MEDR.TN.
Retrocopy LLSRKTTKGIVKQDLMIRK<IPFKLMDVGGKWSWHQKWFQCFDGIMYILFMVSSN<LED*VFMEDRCTNW

Parental  LVES-MNIFETIVNNKLFFNVSIILFLNKMDLLVEKVKTVSIKKHFPDFRGDPHRLEDVQRYLVQCFDRK
          LVES..NIFETIVN.KLFFNVSIILFL.K..LL.EKVK.VSIKKHFPDF.GD.H.L.D.Q.YLVQC..RK
Retrocopy LVES<RNIFETIVNSKLFFNVSIILFLSKLELLIEKVKMVSIKKHFPDFKGDTHKLDDGQCYLVQCSERK

Parental  RRNRSKPLFHHFTTAIDTENIRFVFHAVKDTILQENLKDIMLQ
          ..N.SKPLFHHF.TAI..ENI.F.F..VKDTILQENLKDIM.Q
Retrocopy G*NCSKPLFHHFVTAINRENIYFMFQTVKDTILQENLKDIMFQ

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_653 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,