RetrogeneDB ID: retro_chof_1409

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_28463:388..792(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf1
• Ensembl ID: ENSCHOG00000003039
• Aliases: None
• Description: chromosome 11 open reading frame 1 [Source:HGNC Symbol;Acc:1163]

Sequence

>retro_chof_1409
AGACAGTGCCTCACTTATATCATGAGAAACCCACACTATGGCAACCTCATTAATGTAGATGGCCATGCTGAAGTATGGAC
AGATTGGAATGATATGTCCAAGTTTTTCCAGTATGGACGGAGATGTACCACTAATGAGAATGCATATTCGAACCGTACTT
TGATGGGCAACTAGAACCAGGAAAGATATGACCTAAGAAATATTGTGCAGCCAAAACCCATACCCTCCCAGTTTGGACAC
TACTTTGAAACAACATAAGATGCAAGCTACAACAAAATGCCACTTTCCACCCATAGATTTAAGCGAGAGCCTACTGGTTT
CCAGGAAATCAAGCTGAACTGGATTCTCCTTGATACAAATGCACAGAAAAGTCTACTTATATGAATAGCTATTCAAAGCC
TCAA

Alignment

ORF - retro_chof_1409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RHSLTYILRNPHCGSLINADGHAEV-TDWNDMSKFFQYGWRCTTNENAYSNHTLMGNWNQERYDLRNIMQ
          R..LTYI.RNPH.G.LIN.DGHAEV.TDWNDMSKFFQYG.RCTTNENAYSN.TLMGN.NQERYDLRNI.Q
Retrocopy RQCLTYIMRNPHYGNLINVDGHAEVWTDWNDMSKFFQYGRRCTTNENAYSNRTLMGN*NQERYDLRNIVQ

Parental  PKPLPSQFGHYFETTYDASYNKMSLSTHRFKQEP-HWFPGHQPELDPPQYKCTEKSTYMNSYSKPQ
          PKP.PSQFGHYFETT.DASYNKM.LSTHRFK.EP..WFPG.Q.ELD.P.YKCTEKSTYMNSYSKPQ
Retrocopy PKPIPSQFGHYFETT*DASYNKMPLSTHRFKREP<YWFPGNQAELDSP*YKCTEKSTYMNSYSKPQ

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_1409 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003039	3 retrocopies	retro_chof_1409 , retro_chof_1629, retro_chof_888,
Cavia porcellus	ENSCPOG00000021163	1 retrocopy	retro_cpor_455,
Erinaceus europaeus	ENSEEUG00000009977	1 retrocopy	retro_eeur_658,
Mus musculus	ENSMUSG00000037971	1 retrocopy	retro_mmus_3061,