RetrogeneDB ID: retro_chof_469

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_11276:15366..15920(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBPL1
• Ensembl ID: ENSCHOG00000007544
• Aliases: None
• Description: TBP-like 1 [Source:HGNC Symbol;Acc:11589]

Sequence

>retro_chof_469
ATGAATGCAGACAGCGATGTTGCATTGAACATTCTGATTACAAACATAGTCCGTGTTTTTAGAACAAGAAGCCCTTTGAA
CTTAAGGAAGATTGCTTTGGAGGGAGCAAATGTAATTCATAAGCGTGATGTTGGAAAAGTATTAATGAAGCTTAGAAAAC
CTAGAATTACAGCTACAATTTAGTGCTCAGGAGAAATTATTTGCACTGGAGCAGCAAGTGAAGAAGAAGCTAAATTTGGT
GCCAGACGTTTAGTGTGCAGTCTGCAGAAACTAAGTTTTCAGGTAATGTTTACAGATTTTAAAATTGTTAACGTTTTGGC
AGTGTGTAACATGTCGTTTGAAACCCATTTGCCAAAATTCACAAACAGCAGACTTCCTGCCAGTTACGAACCTGAACTTC
ATCCTGCAGTGTGCTATCGAATGAAATCTCTAAGAGCTACAGTGCAGATTTTCTCAACAGGAAGTATCACAGTTACGTGG
CCCAGCTTCAAGGCTGTGGCTACCTCTTGGAACAGATTTACCTGTTTGTGTTTGAAAGCAGGAAAGACATTTTA

Alignment

ORF - retro_chof_469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDADSDVALDILITNVVCVFRTRCHLNLRKIALEGANVIYKRDVGKVLMKLRKPRITATIWSSGKIICTG
          M.ADSDVAL.ILITN.V.VFRTR..LNLRKIALEGANVI.KRDVGKVLMKLRKPRITATI..SG.IICTG
Retrocopy MNADSDVALNILITNIVRVFRTRSPLNLRKIALEGANVIHKRDVGKVLMKLRKPRITATI*CSGEIICTG

Parental  ATSEEEAKFGARRLARSLQKLGFQVIFTDFKVVNVLAVCNMPFEIRLPEFTKNNRPHASYEPELHPAVCY
          A.SEEEAKFGARRL..SLQKL.FQV.FTDFK.VNVLAVCNM.FE..LP.FT.N.R..ASYEPELHPAVCY
Retrocopy AASEEEAKFGARRLVCSLQKLSFQVMFTDFKIVNVLAVCNMSFETHLPKFT-NSRLPASYEPELHPAVCY

Parental  RIKSLRATLQIFSTGSITVTGPNVKAVATA-VEQIYPFVFESRKEIL
          R.KSLRAT.QIFSTGSITVT.P..KAVAT...EQIY.FVFESRK.IL
Retrocopy RMKSLRATVQIFSTGSITVTWPSFKAVATS<LEQIYLFVFESRKDIL

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_469 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007544	1 retrocopy	retro_chof_469 ,
Cavia porcellus	ENSCPOG00000011899	1 retrocopy	retro_cpor_575,
Echinops telfairi	ENSETEG00000015892	1 retrocopy	retro_etel_1883,
Monodelphis domestica	ENSMODG00000017515	1 retrocopy	retro_mdom_1220,
Otolemur garnettii	ENSOGAG00000006622	2 retrocopies	retro_ogar_1508, retro_ogar_1509,