RetrogeneDB ID: retro_chof_2229

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_59798:6414..7456(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000004467
• Aliases: None
• Description: None

Sequence

>retro_chof_2229
GTAATCGGTACACCTCAGAGATCCGTAGCGCCAAATACTGTCCTGGTAGGAAGTCAACACACCCCTAACACACACTTTGT
ATCACAGAACCAGGCTTCAGACTCCTCAGCTTGGTCTTCTGGGAAACGCAACAGCAAAGGAGAGAAGAATGGCAAGAGTC
TGAGGCATTGTTCAATGAAGGTTTGTGAGAAGGTTCGGAGGAAAGGAACCACTTCCTGTAAGGAAGAGGCAGATGATTTG
GTTGTGGAGCTCAGTGCTGCTGATAACCATATTTTACGAAATGAATCAGCTTATGACCAGAAGAATATAAGAGGACGAGT
CTACGATGCCTCAAATGTCTTAATGGTCATGAATATTATCTCCAAGGACAAAAAAGAAATCAAATGGATTGGTCTGCCTA
CCAACTCGGCTCAGTAATGTCAGAATTTAGAGGTAGAGAGACAGAGAAGACTTGAAAGAATAAAACAGAAACAGTCTCAA
CTTCAGGAACTTATTCTATAGCAAATTGCCTTCAAGAATATGGTGCAGAGAAACTGCCAAGCAGAGCAGCAAGCGAACGG
GCTGCCTCCCTGCAACTCCATCTTCCACCTCCCGTTCATCCTCGTGAACACCAGCAAGAAGACATTGATCAGCTGCAGTA
TTTCTAATGACCAATTTGAGTGTCTGTTTAATTTTGACAACACGTTTGAAATCCATGATGACATAGAAGTATTAAAGCCA
ATGGGAATGGCTTGTGGATTAGAATCAGGAAGCTGTTTGGCCAAAGACCTTAAAATGGCAAGAAGTTTGGTGCTTAAAGC
TCTGGAACCTTATTTGACAGAAATGGCTCAGGGATCAATCAGCGGTGTATTTGTCACATCACAGGTTCAACTTCAAATGG
CACAAGGCTTTCTGCCAGTGACTTGACCAATGGTGCAGACGGGACATTGGCGGCAAGTTCCAGGGGTCTCAGTACAGCGG
CTCCAGGGTGGAGACGCCCGTGTCTTATGTCAGGAAAGAAGATGACAATGACAATGACTTTAACGAAAATGACGAAGAAG
AT

Alignment

ORF - retro_chof_2229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VIGTPQRPAAPNTILVGSPHTPNTHFVSQNQASDSSPWSAGKRNRKGEKNGKGLRHFSMKVCEKVQRKGT
          VIGTPQR..APNT.LVGS.HTPNTHFVSQNQASDSS.WS.GKRN.KGEKNGK.LRH.SMKVCEKV.RKGT
Retrocopy VIGTPQRSVAPNTVLVGSQHTPNTHFVSQNQASDSSAWSSGKRNSKGEKNGKSLRHCSMKVCEKVRRKGT

Parental  TSYNEVADELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQEC
          TS..E.AD.LV.E.SAADNHIL.NESAYDQKNIR.RVYDA.NVLM.MNIISK.KKEIKWIGLPTNSAQ.C
Retrocopy TSCKEEADDLVVELSAADNHILRNESAYDQKNIRGRVYDASNVLMVMNIISKDKKEIKWIGLPTNSAQ*C

Parental  QNLEVERQRRLERIKQKQSQLQELILQQIAFKNLVQRNRQAEQQANRPPPSNSVIHLPFIIVNTSKKTVI
          QNLEVERQRRLERIKQKQSQLQELIL.QIAFKN.VQRN.QAEQQAN..PP.NS..HLPFI.VNTSKKT.I
Retrocopy QNLEVERQRRLERIKQKQSQLQELIL*QIAFKNMVQRNCQAEQQANGLPPCNSIFHLPFILVNTSKKTLI

Parental  DCSISNDKFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSA-DL-MARSLVPKALEPYVTXXXXXXX
          .CSISND.FE.LFNFDNTFEIHDDIEVLK.MGMACGLESGSC.A.DL.MARSLV.KALEPY.T.......
Retrocopy SCSISNDQFECLFNFDNTFEIHDDIEVLKPMGMACGLESGSCLAKDLKMARSLVLKALEPYLTEMAQGSI

Parental  XXXXXTS-SGSTSNGTRLSASDLTNGADGTLATSS-SGSQYSGSRVETPVSYVGEDDDDDDDFNENDDED
          .....TS..GSTSNGTRLSASDLTNGADGTLA.SS..GSQYSGSRVETPVSYV...DD.D.DFNEND.ED
Retrocopy SGVFVTS<TGSTSNGTRLSASDLTNGADGTLAASS<QGSQYSGSRVETPVSYVRKEDDNDNDFNENDEED

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_2229 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 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229 , retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243, retro_mmus_338,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314, retro_pabe_132, retro_pabe_378,