RetrogeneDB ID: retro_chof_376

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_101380:499..1097(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT5
• Ensembl ID: ENSCHOG00000005142
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 5 [Source:HGNC Symbol;Acc:20886]

Sequence

>retro_chof_376
ATGTTTCTTGTGATTTTTCCAGAGGGAACAAGGGTATAATCTGGACCTAAGAAAAATCATTTCAGTCAGTCAAACTTTTG
CTGCTCAAAAATGCCTTTCAGTATTGCAATGTGTGCCAACACCAACAGTAAAGGGAACTCATGCTGCTTTTGAGTCTATG
AAGAATTATTTAAATGCAGTTTATGATGTTACAGTGGCTTATGAAAGGGATCATGGATGATAAAGGTTGGCAAAAAGAAG
CACCGTCCATGACTGAATTTCTCTGCAAAGAATGTACAAAAACTTGTATTCACATTGATCATATAAACAAAAAAGATATC
CTGGAAGACAAGTATATATGAGAAGATGGTTTCATGAACATTTTGAAATAAAAGATAAATTGCTTATAGACTTTTATGAT
TCAATTGATCCAGAAAGGACAAGCAAATTTCTTGGGGAAAGTGTTAAGTCCAAACTAAGTCTCAAAAAGACTTTATCATC
ATTATAGATCTTAAGTGGTTTGACGGCTAGTATGCTTATGATACAGGCTAGAAGGAAACTATATGTAAAAATGTGGCTAA
ATGGAATCTTAACTGGCTGCTTATGGGTTATTAAAGCA

Alignment

ORF - retro_chof_376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.34 %
• Parental protein coverage: 58.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFLVIFPEGTR-YNPELTKVISASQAFAAQQGFTVLKHVLTPRVKATHVAFNSMKNYLDAIYDVTVAYE-
          MFLVIFPEGTR.YN..L.K.IS.SQ.FAAQ....VL..V.TP.VK.TH.AF.SMKNYL.A.YDVTVAYE.
Retrocopy MFLVIFPEGTR>YNLDLRKIISVSQTFAAQKCLSVLQCVPTPTVKGTHAAFESMKNYLNAVYDVTVAYE>

Parental  GTIDDKGQRKEAPSMTEFLC-ECPKIHIHID-IDKKDVLEEP-ADMRRWLREGFEIKDKLLIESYDSLDP
          G..DDKG..KEAPSMTEFLC.EC.K..IHID.I.KKD.LE.....MRRW..E.FEIKDKLLI..YDS.DP
Retrocopy GIMDDKGWQKEAPSMTEFLCKECTKTCIHIDHINKKDILEDK<VYMRRWFHEHFEIKDKLLIDFYDSIDP

Parental  ERRNEFPGENVNSKLNPKKNLPSLLTLSGLAASMLMTEARWKLYVQT-IYGTLIGCLVSIKA
          ER...F.GE.V.SKL..KK.L.SL..LSGL.ASMLM..AR.KLYV.....G.L.GCL..IKA
Retrocopy ERTSKFLGESVKSKLSLKKTLSSL*ILSGLTASMLMIQARRKLYVKMWLNGILTGCLWVIKA

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_376 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005142	1 retrocopy	retro_chof_376 ,
Dasypus novemcinctus	ENSDNOG00000004979	1 retrocopy	retro_dnov_823,
Dipodomys ordii	ENSDORG00000008708	1 retrocopy	retro_dord_523,
Otolemur garnettii	ENSOGAG00000008958	1 retrocopy	retro_ogar_3477,
Ochotona princeps	ENSOPRG00000014343	3 retrocopies	retro_opri_343, retro_opri_829, retro_opri_935,
Pongo abelii	ENSPPYG00000018320	1 retrocopy	retro_pabe_3671,
Sarcophilus harrisii	ENSSHAG00000000051	1 retrocopy	retro_shar_687,
Tupaia belangeri	ENSTBEG00000013084	1 retrocopy	retro_tbel_2948,