RetrogeneDB ID: retro_chof_2313

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_6541:5314..6280(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT7
• Ensembl ID: ENSCHOG00000007937
• Aliases: None
• Description: chaperonin containing TCP1, subunit 7 (eta) [Source:HGNC Symbol;Acc:1622]

Sequence

>retro_chof_2313
CCCACACCAGTTATCCTGTTGAAAGAGGGGACTGACAGTTCCCAAGGCATCCCCCAGCTTGTAAGTAATATCACCGCCTG
CCAGGTGATTGCCGAGGCTGTAAGAACCACTCTGGGTCCCCGTGGCATGGACAAGCTCATTGTGGATGGCCGAGGCAAAG
CAACAATATCTAATGATGGGGCCACAATTCTGAAACTCCTTGATGTCATCCATCCTGCAGCAAAGACTTTAGTGGACATT
GCCAAATCCCAAGATGCTGATGTCAGTGATGGCACCACCTCAGTGACCCTGCTGGCTGTAGAGTTCCTGAAGCAGGTGAA
ACCATATGAGGAGGAAGGTTTGCACCCACAGATCATCATCCGAGCTTTCCACACTGCCACACATTTCGCAGTTAACAAGA
TCAAAGAGATTTCTGTGACCGTGAAGAAGGAAGATAAAGTGGAGCAGAGGAAGCTACTGGAGAAGTGTGCCATGACCACT
TTGAGCTCCAAGCTGATCTCCCAGCAGAAAGCCTTCTTTGCTAAGATGGTGGTTGATGCGGTGATGATGCTTGACAATTT
GCTGCAGCTCAAAATTATTGGAATCAAGAAAGTGCAGGGCGGAGCCCTAGAGGAGTCCCAGCTGGTAGCTGGTGTTGCAT
TCAAGAAGACTTTCTCTTATGCTGGGTTTGAAATACAACCCAAAAAGTATGATAATCCCACAATTGCCCTTTTAAATGTT
GAGCTTGAGCTGAAAGCTGAGAAAGATAATGCTGAAGTCAGAGTCCACACAGTTGAGGATTATCAGGTGACTGCTGATAC
TGAGTGGAACATTCTCTATGACAAGTTAGAGAAGATCCATGCTTCAGGAGCCAAAGTTGTTTTGCCCAAACTCCCCATTG
GGGATGTGGCTACCCAGTACTTTGCTGACAGGGACATGTTTTGTGCTGGCCAAGTGCCCGAGGAGGATCTGAAGAGAACA
ATGATG

Alignment

ORF - retro_chof_2313 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.37 %
• Parental protein coverage: 77.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTPVILLKEGTDSSQGIPQLVSNITACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDVI
          PTPVILLKEGTDSSQGIPQLVSNITACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDVI
Retrocopy PTPVILLKEGTDSSQGIPQLVSNITACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDVI

Parental  HPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATHLAVNKIKEIAVT
          HPAAKTLVDIAKSQDA.V.DGTTSVTLLA.EFLKQVKPY.EEGLHPQIIIRAF.TATH.AVNKIKEI.VT
Retrocopy HPAAKTLVDIAKSQDADVSDGTTSVTLLAVEFLKQVKPYEEEGLHPQIIIRAFHTATHFAVNKIKEISVT

Parental  VKKEDKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVMMLDDLLQLKMIGIKKVQGGALEESQLVA
          VKKEDKVEQRKLLEKCAMT.LSSKLISQQKAFFAKMVVDAVMMLD.LLQLK.IGIKKVQGGALEESQLVA
Retrocopy VKKEDKVEQRKLLEKCAMTTLSSKLISQQKAFFAKMVVDAVMMLDNLLQLKIIGIKKVQGGALEESQLVA

Parental  GVAFKKTFSYAGF-MQPKKYDNPTIALLNVELELKAXXXXXXXXXXXXXDYQAIVDAEWNILYDKLEKIH
          GVAFKKTFSYAGF..QPKKYDNPTIALLNVELELKA.............DYQ...D.EWNILYDKLEKIH
Retrocopy GVAFKKTFSYAGFEIQPKKYDNPTIALLNVELELKAEKDNAEVRVHTVEDYQVTADTEWNILYDKLEKIH

Parental  ASGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMM
          ASGAKVVL.KLPIGDVATQYFADRDMFCAG.VPEEDLKRTMM
Retrocopy ASGAKVVLPKLPIGDVATQYFADRDMFCAGQVPEEDLKRTMM

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_2313 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151,
Choloepus hoffmanni	ENSCHOG00000007937	1 retrocopy	retro_chof_2313 ,
Echinops telfairi	ENSETEG00000009409	2 retrocopies	retro_etel_1478, retro_etel_607,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708, retro_tbel_3751,