RetrogeneDB ID: retro_chof_379

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_101746:3279..3717(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000011899
• Aliases: None
• Description: None

Sequence

>retro_chof_379
CTGGGATGTCCAGTCTGCAAATCAGATGTCCTTTCCCAGATGATACAAGGAAAGGAGGTGTGGAGAGAAGGAATAGGATT
TCTTCAAAACTGGAGTCCAGCCAGGAAAAGTGCCAGTAAAATGCAAGAAGTAGTATTGCCGCAACTTACATACAGAAAGG
AAAATTCTAACGTCATATCATTGCAGATATCACACGCTCAAAAGAATCCCTTTCAATGCAATTATTTGCAAGAAGATTCC
ACTCTCAGATCCACAGTAACTCACCATGCATTATTTCCCATGAGAAAGAAACCATATTTAAGCACACCACTTGGAAAACT
CCTTGGTGACCACTCATGTTTTAATCAACATGAGCACATTCCAACTGAAAGTAAATCATATGAGAGTCATTGGAGTGTTA
AAGACATTACTAAAAGCTCTGGCCACAGGAAATCCAAT

Alignment

ORF - retro_chof_379 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.03 %
• Parental protein coverage: 56.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGCQVCKSDVL-QMVQGEEVWREGVDSLQNQSPGRKNARKMQEMILLQLTCRKENSNLMLLQKSHTQKNS
          .GC.VCKSDVL.QM.QG.EVWREG...LQN.SP.RK.A.KMQE..L.QLT.RKENSN...LQ.SH.QKN.
Retrocopy LGCPVCKSDVLSQMIQGKEVWREGIGFLQNWSPARKSASKMQEVVLPQLTYRKENSNVISLQISHAQKNP

Parental  FQCISLQEDSTLRSPVTQHALFPMRKKPYLSKPLGKLLGDHSSFNQHEQIPAESKSYEGHQSVKAITKSC
          FQC..LQEDSTLRS.VT.HALFPMRKKPYLS.PLGKLLGDHS.FNQHE.IP.ESKSYE.H.SVK.ITKS.
Retrocopy FQCNYLQEDSTLRSTVTHHALFPMRKKPYLSTPLGKLLGDHSCFNQHEHIPTESKSYESHWSVKDITKSS

Parental  GHRNSN
          GHR.SN
Retrocopy GHRKSN

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_379 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	ENSCHOG00000007736	2 retrocopies	retro_chof_154, retro_chof_2671,
Choloepus hoffmanni	ENSCHOG00000011097	2 retrocopies	retro_chof_1923, retro_chof_228,
Choloepus hoffmanni	ENSCHOG00000011899	1 retrocopy	retro_chof_379 ,
Homo sapiens	ENSG00000196946	1 retrocopy	retro_hsap_2965,