RetrogeneDB ID: retro_chof_228

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5043:51226..51726(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000011097
• Aliases: None
• Description: None

Sequence

>retro_chof_228
TGTGAGGTCTGGAAATCAGATGTGTTTTCCCTTTTGGCACAGAAACAGGTAGTGTGGAGGGAAGGAATGGAATTTCTTCA
AAACCAAAGCCCAGGTGTGGAAATTGCCTGTAAAAAGCAAGAGATGATATTAATGCAACTTACCTACAGAAATGACAATT
CTGAGGATGCATAATTGATTTTTCAGACTCAGAAGAATTCCTTTAAATGTAATTATTTGCAAGAAGATTCCACCCTCAGA
TCCAAAGTGATTCAACATGCATTAATTCCCATGAGATAGAAACCATCTTCATGCAAGCCACTTGGAAAAGTCCTCAGTGA
CCAGTCATCTTTTAAAAACTTGAGCAGATTCACACTGCAAGTAAATCCTATGAATGCTGTGAAAATGCTATGGCCTTTAT
TGAAAACACTGGCCAAAAACAGTATGGTGGAAATCAAAGTGGAGATAAGCCATGTGGATGCTTTCTGTGTGGGAAATCAT
TCTTTGGATTTGTTGACTTT

Alignment

ORF - retro_chof_228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.37 %
• Parental protein coverage: 88.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CKVCISDVFSLLAQKQVMWREGMEFLRNQSPGMEIACKKQEMIFMQLIYRNDNSEDASLRISYTQKNSFK
          C.V..SDVFSLLAQKQV.WREGMEFL.NQSPG.EIACKKQEMI.MQL.YRNDNSEDA.L.I..TQKNSFK
Retrocopy CEVWKSDVFSLLAQKQVVWREGMEFLQNQSPGVEIACKKQEMILMQLTYRNDNSEDA*L-IFQTQKNSFK

Parental  FNYLQEDSTLRSAVTQHALIPMRKRPYLRKPFGKVLSEQSSFN-KHEQFHTGSKSYECHRNVKAFIKNAG
          .NYLQEDSTLRS.V.QHALIPMR..P...KP.GKVLS.QSSF..K.EQ.HT.SKSYEC..N..AFI.N.G
Retrocopy CNYLQEDSTLRSKVIQHALIPMR*KPSSCKPLGKVLSDQSSFK<KLEQIHTASKSYECCENAMAFIENTG

Parental  HKEYDRAQTGDKAYKCFLCGKAFIGFMDF
          .K.Y...Q.GDK...CFLCGK.F.GF.DF
Retrocopy QKQYGGNQSGDKPCGCFLCGKSFFGFVDF

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_228 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,