RetrogeneDB ID: retro_chof_272

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5980:12796..13519(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT2
• Ensembl ID: ENSCHOG00000006098
• Aliases: None
• Description: chaperonin containing TCP1, subunit 2 (beta) [Source:HGNC Symbol;Acc:1615]

Sequence

>retro_chof_272
TTAATTTATAATTACCCGGAACAGCTCTTTGGTGCTGCTGGTGTCATGGCTATTGAGCATGCAGATTTTGCAGGTGTGGA
ACGCCTCGCTCTTGTCACAGGTGGTGAAATTGCCTCTACCTTTGATCACCCAGAGCTAGTAAAGCTTGGAAGTTGCAAGC
TTATTGAGGAAGTCATGATTGGAGAAGACAAACTCATTCACTTTTCTGGGGTAGCCCTTGGTGAGGCTTGCACTATTGTC
CTGCGTGGTGCCACTCAGCAAATTTTAGATGAAGCAGAAAGATCTTTGCATGATGCTCTTTGTGTTCTTGCCCAAACTGT
AAAGGATTCTAGAACAGTGTATGGAGGAGGCTGTTCTGAGATGCTGATGGCGCATGCTGTTACAAAGCTTGCCAGTAGAA
CACCAGGCAAAGAAGCTGTTGCAATGGAATCTTACGCCAAGGCACTGAGAATGTTGCCAACCATCATAGCTGACAATGCA
GGTTACGACAGCGCAGATTTGGTGGCACAGCTTCGAGCTGCCCACAGTGAAGGAAAAATAACTGCTGGACTGGATATGAA
GGAGGGTACCATTGGAGATATGGCTGTTCTGGGTATAACAGAAAGTTTCCAAGTCAAACGACAAGTTCTTTTGAGTGCAG
CTGAAGCAGCAGAGGTGATTCTACGTGTGGATAACATTATCAAAGCAGCACCGAGGAAACGTGTTCCTGATCACCACCCT
TGT

Alignment

ORF - retro_chof_272 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 51.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIHNYPTQAQLSDAAGVMVIEHADFAGVEHLALITGGEIASTFDHPELVKLGSCKLIEEVMIGEDKLIHF
          LI.NYP.Q..L..AAGVM.IEHADFAGVE.LAL.TGGEIASTFDHPELVKLGSCKLIEEVMIGEDKLIHF
Retrocopy LIYNYPEQ--LFGAAGVMAIEHADFAGVERLALVTGGEIASTFDHPELVKLGSCKLIEEVMIGEDKLIHF

Parental  SGVALGEACTIVLRGATQQILDEAERSLHDALCVLAQTVKDSRTVYGGGCSEMLMAHAVTKLASRTPGKE
          SGVALGEACTIVLRGATQQILDEAERSLHDALCVLAQTVKDSRTVYGGGCSEMLMAHAVTKLASRTPGKE
Retrocopy SGVALGEACTIVLRGATQQILDEAERSLHDALCVLAQTVKDSRTVYGGGCSEMLMAHAVTKLASRTPGKE

Parental  AVAMESYAKALRMLPTIIADNAGYDSADLVAQLRAAHSEGKITAGLDMKEGTIGDMAVLGITESFQVKRQ
          AVAMESYAKALRMLPTIIADNAGYDSADLVAQLRAAHSEGKITAGLDMKEGTIGDMAVLGITESFQVKRQ
Retrocopy AVAMESYAKALRMLPTIIADNAGYDSADLVAQLRAAHSEGKITAGLDMKEGTIGDMAVLGITESFQVKRQ

Parental  VLLSAAEAAEVILRVDNIIKAAPRKRVPDHHPC
          VLLSAAEAAEVILRVDNIIKAAPRKRVPDHHPC
Retrocopy VLLSAAEAAEVILRVDNIIKAAPRKRVPDHHPC

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_272 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000432	2 retrocopies	retro_cfam_1969, retro_cfam_2166,
Choloepus hoffmanni	ENSCHOG00000006098	1 retrocopy	retro_chof_272 ,
Callithrix jacchus	ENSCJAG00000001715	2 retrocopies	retro_cjac_1854, retro_cjac_2579,
Loxodonta africana	ENSLAFG00000006688	1 retrocopy	retro_lafr_351,
Myotis lucifugus	ENSMLUG00000008364	1 retrocopy	retro_mluc_2248,