RetrogeneDB ID: retro_chof_1045

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_189661:0..768(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP11L1
• Ensembl ID: ENSCHOG00000002495
• Aliases: None
• Description: t-complex 11, testis-specific-like 1 [Source:HGNC Symbol;Acc:25655]

Sequence

>retro_chof_1045
TTTTCTGTGGTGGGCCTAATGAAAGTGGACATGGCAAAACTTGCAGTCAGTAGCATTAGGCCACATCTCATGCAGCAGTT
GGTTGAATATGAAAGGAAGACGTTTCAAGAGATTTTGGAGAAGCAACCAAACTCCCTGGATTTTGTTACTCAGTGGCTAG
AAGAAGCTGCAGATGACCTTATAAATTAGAAGTATAGAAATATCCTGCCCACTGTAGGAGGGGCTGCTTGCTCTGGCAAT
GTTACACTGCCAAGTCCTGTTGCTGTCCAGAAGTATGCCTACTTGAAATTTTGAAATGGATCCACATCCAGAGATCTTTC
CCTGAAACAATTTTCATGGACCAGTCTCACTTCCAAGAGCTTCAGCTTTAGCTGGAGCATCTAACCATCCTGGAGACCAT
ATTGCTGGTCAGGTTCAGCATGGTAGCCCCAGGAATTTGATTCCAAGTAGATTTTGCTGGGAAATTCAAGATGATTGTCA
AGATTCTGCTAACAGGTAAGCATCTCCTGTCCTTCAATCTGAAGGATGCACTGACTACCATTGGGGAGAAAGTCTGCATG
GAAGTGGGCAGCTGCCTTTCCCTTGTGTTCTGACAAGGAGACAGTGCTCAAGGGCTAGATTCAGGCTCTGGCCAGTCCTA
ATGACCCCATTTTCAGGATCATGGATTCTCCTATCCTAACCTTAGAAATCTACCTTGCCTCAGGTCATCAGAAGCCATTC
CCTACAGTATCTGGTGGGTTGAGTCAAGTACAGAAAGAGCTAGAGGAA

Alignment

ORF - retro_chof_1045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.92 %
• Parental protein coverage: 51. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FSVLGLMKVDMANFAVSSIMPHLMQQSVEYEEK-FHELLE-QPNSLDFVTQWLEEAADDLMNQKCRNSLP
          FSV.GLMKVDMA..AVSSI.PHLMQQ.VEYE.K.F.E.LE.QPNSLDFVTQWLEEAADDL.N.K.RN.LP
Retrocopy FSVVGLMKVDMAKLAVSSIRPHLMQQLVEYERKTFQEILEKQPNSLDFVTQWLEEAADDLIN*KYRNILP

Parental  AIGGAACSGDVTVPSPVAVQNYAYLK-LLKWDHLQRPFPETVLMDQSRFQELQLQLEHLTVLGAVLLVTF
          ..GGAACSG.VT.PSPVAVQ.YAYLK..LKW.H.QR.FPET..MDQS.FQELQL.LEHLT.L...LLV.F
Retrocopy TVGGAACSGNVTLPSPVAVQKYAYLK<ILKWIHIQRSFPETIFMDQSHFQELQL*LEHLTILETILLVRF

Parental  SMVAPGISFQAEFAGKLKMIVKILLTDMHLPSFHLKDALTTIGEKVCMEVGSCLSL-CSDKETVLKGQIQ
          SMVAPGI.FQ..FAGK.KMIVKILLT..HL.SF.LKDALTTIGEKVCMEVGSCLSL.CSDKETVLKG.IQ
Retrocopy SMVAPGI*FQVDFAGKFKMIVKILLTGKHLLSFNLKDALTTIGEKVCMEVGSCLSL>CSDKETVLKG*IQ

Parental  AVASPDDPIRRIMDSRILTFLETYLASGHQKPFPTVPGGLGPVQKELEE
          A.ASP.DPI.RIMDS.ILT.LE.YLASGHQKPFPTV.GGL..VQKELEE
Retrocopy ALASPNDPIFRIMDSPILT-LEIYLASGHQKPFPTVSGGLSQVQKELEE

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_1045 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	ENSCHOG00000002495	1 retrocopy	retro_chof_1045 ,