RetrogeneDB ID: retro_chof_1757

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_37725:4636..5290(-)
• 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_1757
GGCTCTTCTGCTAAGCCTCTGATGTCTTCTGACAATTGCATACTCCAGTGGGGATTTTAGACTTACAGGACCTCCTCCTT
ATGGAATAGCTTCCAGTACCAATTCGAGTGGGCAAGAGAATAATTCTGCCCAAAGCGCTCAGCTTCCTTCCATGAATGAA
CAGTCACAGAAGACATGAGGGACACCCAACTTTGATTCAGAGCTGTCTTTAGAAAAACTGGAAGATTTGCCTCCGTTGTC
CCCATTGCAACCAATTTCCAAGAAGAGGCTGTTCAAATTATTGCAGATCCTCTGTTACCCCAGTTTTAGTCACACTTCAA
GACATTCTGGATCATTCTGACACTCTGCAGGAGTTAGTGGTTCTAGGGGTGGATTTGCCCAAGATAGAAAAACATCCTGA
TGCAGCCAACCAACTTCTGAGACTGGAATTTGAGAATTTGAGAAAATACTCCTGCTTCTTAAAGATTTGGGTATAGAGCG
TGACCAACTGTGAGCATTCCTGACTAAAAGGTATGCCATTTTCTCTGAAGACCTTGAAAACCTTAAGACCAGGGTGGCTT
ACCTACAGTCAAAAAATTTCAGTAAGGAAATAGTGCACAGATAGTCAGAAATGCACCATTTTTGCTGAGTTTTTCAGTGG
AAAGGCTGGATAAC

Alignment

ORF - retro_chof_1757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.66 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GSSAKPLISSDNGVLQWGFKTFTTSSLWNSFQH-TNTSRQENNSAQSTQLPSVNEQSQKT-QTPNFDSEL
          GSSAKPL.SSDN..LQWGF.T..TSSLWNSFQ.........N.SAQS.QLPS.NEQSQKT..TPNFDSEL
Retrocopy GSSAKPLMSSDNCILQWGF*TYRTSSLWNSFQY>NSSGQENN-SAQSAQLPSMNEQSQKT*GTPNFDSEL

Parental  CLEKLEDLPPLSPLQPISEK-EAIQIIADPLLP-PVSFTLRDYVDHSETLQKLVLLGVDLSKIEKHSDAA
          .LEKLEDLPPLSPLQPIS.K.EA.QIIADPLLP.PV..TL.D..DHS.TLQ.LV.LGVDL.KIEKH.DAA
Retrocopy SLEKLEDLPPLSPLQPISKK<EAVQIIADPLLP<PVLVTLQDILDHSDTLQELVVLGVDLPKIEKHPDAA

Parental  NHLLRLDFEKDFKK-ILLFLKDLGIEDNQLGAFLTKNYAIFSEDLENLKIRVAYLQSKKFSKTDI-AQMV
          N.LLRL.FE....K.ILL.LKDLGIE..QL.AFLTK.YAIFSEDLENLK.RVAYLQSK.FSK....AQ.V
Retrocopy NQLLRLEFE-NLRK<ILLLLKDLGIERDQL*AFLTKRYAIFSEDLENLKTRVAYLQSKNFSKEIV<AQIV

Parental  RKAPFLLSFSVERLDN
          R.APFLLSFSVERLDN
Retrocopy RNAPFLLSFSVERLDN

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_1757 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,