RetrogeneDB ID: retro_chof_1333

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_265627:0..913(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTERFD1
• Ensembl ID: ENSCHOG00000007893
• Aliases: None
• Description: MTERF domain containing 1 [Source:HGNC Symbol;Acc:24258]

Sequence

>retro_chof_1333
AGTTTCCAGCTTACCAACTCAAGTCAGAAGTGCTCTGTTTCCTCCCACGAATGATCAGTCACAGGGGACACAAAGGACAC
CCAGCTCTGATTCTGAGCTGTCTCTAGAAGAACTGGAAGCTTTACCTCCATTGTCTCCATTGCAACCAATTTCCAAGAAA
GAGGCTGTTCAAATTATTGCAGACCCTCTGTTGCCCCCAGTTTCATTCACACTTTGAGACTATGTGGATCATTCTGAGAC
TCTGCAGGAGTTAATGCTTCTAGGGGTGGATTTGTCCAAGATAGAAAAACATTCTGATGCAGCCAACCACCTTCTGAGAC
TGGATTTTGAGAAAGACTTTAAGAAAATACTCCTGTTTCTTAAAGATTTGGGTATAGAGGATAACCAACTGGGAGCATTC
TTGACTAAAAAGTATGCCATTTTCTCCGAAGACCTTGAAAATCTTAAGATCAGGGTGGCTTACCTACAGTCAAAACAGTT
CAGTAAGACAGATATTGCACAGATGGTCAGAAAGGCAGCATTTTTGCTGAATTTTTGGTGGAAAGGCTGGATAACAGATT
GGGGTTTTTTTTCAGAAAGAACTTGAACTTAATGTGAAAAAGATGAGAGATCTAGTAATTCCTCTCCCAAGGCTACTAAC
TAGAAGCCTAGAGCTTATGAAAGAAAATATGAAGGTTTATCATCTTGCACTTGGTTTTAAACACAATGAAATTCAACATA
TGATCACCAGAATCCCAAAGACATTAACTGCAAATAAAAGGAAACTTACTGAGACTTTTGATTATGTGCTCAACGTGCTG
TGGATTCCCCACCACATCATTGTAAGGTCCCCACAGGTATTAATACAAAGTTGTTTAAAAATCAAGAAAGACATTTTGTT
TCTTACATATTTAGGAAGAGCCAGTATGATCCA

Alignment

ORF - retro_chof_1333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.32 %
• Parental protein coverage: 72.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SRQENNSAQ-STQLPSVNEQSQKTQ-TPNFDSELCLEKLEDLPPLSPLQPISEKEAIQIIADPLLPPVSF
          S.Q..NS.Q.S...P..N.QSQ.TQ.TP..DSEL.LE.LE.LPPLSPLQPIS.KEA.QIIADPLLPPVSF
Retrocopy SFQLTNSSQ>SALFPPTNDQSQGTQRTPSSDSELSLEELEALPPLSPLQPISKKEAVQIIADPLLPPVSF

Parental  TLRDYVDHSETLQKLVLLGVDLSKIEKHSDAANHLLRLDFEKDFKKILLFLKDLGIEDNQLGAFLTKNYA
          TL.DYVDHSETLQ.L.LLGVDLSKIEKHSDAANHLLRLDFEKDFKKILLFLKDLGIEDNQLGAFLTK.YA
Retrocopy TL*DYVDHSETLQELMLLGVDLSKIEKHSDAANHLLRLDFEKDFKKILLFLKDLGIEDNQLGAFLTKKYA

Parental  IFSEDLENLKIRVAYLQSKKFSKTDIAQMVRKAPFLLS-FSVERLDNRLG-FFQKEL-ELNVKKTRDLVI
          IFSEDLENLKIRVAYLQSK.FSKTDIAQMVRKA.FLL..F.VERLDNRLG....K.L.ELNVKK.RDLVI
Retrocopy IFSEDLENLKIRVAYLQSKQFSKTDIAQMVRKAAFLLN<FLVERLDNRLGXXXRKNL<ELNVKKMRDLVI

Parental  RLPRLLTGSLEPVKENMKVYRLELGFKHNEIQHMITRIPKMLTANKRKLTDTFDYVHNVMQIPHHIIVRF
          .LPRLLT.SLE..KENMKVY.L.LGFKHNEIQHMITRIPK.LTANKRKLT.TFDYV.NV..IPHHIIVR.
Retrocopy PLPRLLTRSLELMKENMKVYHLALGFKHNEIQHMITRIPKTLTANKRKLTETFDYVLNVLWIPHHIIVRS

Parental  PQV-FNTKLLKIKERH-LFLTYLGRA-QYDP
          PQV..NTKL.K..ERH.LFLTYLGRA.QYDP
Retrocopy PQV<INTKLFKNQERH>LFLTYLGRA<QYDP

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_1333 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007893	3 retrocopies	retro_chof_1333 , retro_chof_1757, retro_chof_2268,
Erinaceus europaeus	ENSEEUG00000004188	1 retrocopy	retro_eeur_123,
Otolemur garnettii	ENSOGAG00000004303	1 retrocopy	retro_ogar_3409,