RetrogeneDB ID: retro_chof_944

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_17332:13907..14453(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TERF1
• Ensembl ID: ENSCHOG00000002407
• Aliases: None
• Description: telomeric repeat binding factor (NIMA-interacting) 1 [Source:HGNC Symbol;Acc:11728]

Sequence

>retro_chof_944
GCAGCAGCAAAAGTAGCGGAAAGTAAAAGATCAAGAACAGTAACCGCTCAAGATAAACCTAACGGTAATAATAACGAAAT
GGAAACTGAAGCTAATTTGTGTATAAGAAAAAGTGTTAGTGACACACAGTCTGCAGTAACTGAATCCTCAGAGGGTACAG
TATCCTTACTGAGGTCTCACAAGAATCTCTTCTTATCTAAGTTTAAACATGGAACCCAACAACAAGATCTTGATAAGAAA
GAGGAAAGAGCAGGAACTCTTCAAAGTAAAAGAAAGAAAGAAGAAAACTGTAGAAGAGTCCCTGGAAGCAAGAGACTTCA
TGTTTTAAACAGTCAGCCAGTATCTGCTGAAAAACATTGATCTAGAAAAAAACAGGCATGGCTTTGGGAAGAAGACAAGA
ATCTGTGATCTGGCATGAAGAAATACAGGGAGGGAAACTGGTCTAAAATATTATTACATTATAAATTCAACAACCAAACA
AGCGTCATGCTAAAAGACAGATGGAGGACTATGAAGAAACTAAAACTGATTTGCTCAGACAGTGAT

Alignment

ORF - retro_chof_944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 54.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAKVVESKRSRTVTAQDKPNGNNNETETEANLYIRKSVNDTQSAVTESSEGTVSLLRSHKNLFLSKFKH
          AAAKV.ESKRSRTVTAQDKPNGNNNE.ETEANL.IRKSV.DTQSAVTESSEGTVSLLRSHKNLFLSKFKH
Retrocopy AAAKVAESKRSRTVTAQDKPNGNNNEMETEANLCIRKSVSDTQSAVTESSEGTVSLLRSHKNLFLSKFKH

Parental  GTQQQDLDKKEERAGTLQIRRKKEENCRRVPGSKRLHALNNQPVSHEKHRSRKKQAWLWEEDKNLRSGVK
          GTQQQDLDKKEERAGTLQ..RKKEENCRRVPGSKRLH.LN.QPVS.EKH.SRKKQAWLWEEDKNL.SG.K
Retrocopy GTQQQDLDKKEERAGTLQSKRKKEENCRRVPGSKRLHVLNSQPVSAEKH*SRKKQAWLWEEDKNL*SGMK

Parental  KYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKLKLICSDSD
          KY.EGNWSKILLHYKFNN.TSVMLKDRWRTMKKLKLICSDSD
Retrocopy KYREGNWSKILLHYKFNNQTSVMLKDRWRTMKKLKLICSDSD

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_944 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 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002407	1 retrocopy	retro_chof_944 ,
Callithrix jacchus	ENSCJAG00000007714	1 retrocopy	retro_cjac_1658,
Homo sapiens	ENSG00000147601	6 retrocopies	retro_hsap_1166, retro_hsap_1917, retro_hsap_2493, retro_hsap_3099, retro_hsap_4324, retro_hsap_4861,
Oryctolagus cuniculus	ENSOCUG00000002793	1 retrocopy	retro_ocun_546,
Pan troglodytes	ENSPTRG00000022919	7 retrocopies	retro_ptro_1245, retro_ptro_1445, retro_ptro_2095, retro_ptro_3236, retro_ptro_3241, retro_ptro_611, retro_ptro_802,