RetrogeneDB ID: retro_chof_1629

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_345915:429..826(+)
• 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_1629
CTCACTTATATCATGAGACACCCACACTATGAATGCCTCATAAGTGTTAATGACCATGCTGAAGAAAGGACAGATTGGAA
TGATATGTTCAAGTTTTTCCTGTATGGACGGATATGTACCACTAATAAAAATGCCTATTTGAACTAGACTTTGATGGGCA
ACTGGAACCAGGAAAGATATGACCTAAAGGGATATTGTGCAGCCAAAACCCTTACCTTCCCAGTTTGGGCACTATTTTGA
AACAACATATGATGCAAGCTACAACAAAACGCCACTTTCAACCTATAGATTTAAGTGAGAGGCTCACTGGTTTCCAGGAC
ATCAACCCAAACTGGATACTCCTTGATACAAATGCACAGAAAAGGCAACTTATATGAATAGTTATTGAAAGCCTCAA

Alignment

ORF - retro_chof_1629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.69 %
• Parental protein coverage: 97.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTYILRNPHCGSLINADGHAEV-TDWNDMSKFFQYGWRCTTNENAYSNHTLMGNWNQERYDL-RNIMQPK
          LTYI.R.PH...LI....HAE..TDWNDM.KFF.YG..CTTN.NAY.N.TLMGNWNQERYDL.R.I.QPK
Retrocopy LTYIMRHPHYECLISVNDHAEERTDWNDMFKFFLYGRICTTNKNAYLN*TLMGNWNQERYDL>RDIVQPK

Parental  PLPSQFGHYFETTYDASYNKMSLSTHRFKQEPHWFPGHQPELDPPQYKCTEKSTYMNSYSKPQ
          PLPSQFGHYFETTYDASYNK..LST.RFK.E.HWFPGHQP.LD.P.YKCTEK.TYMNSY.KPQ
Retrocopy PLPSQFGHYFETTYDASYNKTPLSTYRFK*EAHWFPGHQPKLDTP*YKCTEKATYMNSY*KPQ

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_1629 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,