RetrogeneDB ID: retro_chof_2469

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_78283:3125..4179(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTPS1
• Ensembl ID: ENSCHOG00000005540
• Aliases: None
• Description: CTP synthase 1 [Source:HGNC Symbol;Acc:2519]

Sequence

>retro_chof_2469
GTCCCTCACATCACAGATGCAATCCAGGAGTGGGTAATGAGGCAGGCATTATCTCCTGTAGATGAAGATGGCCTGGAACC
TCAAGTGTGTGTTATTGAGCTTGGTGGAACGGTGGGAGATATAGAAAGCATGCCCTTTATCGAGGCTTTCCGCCAGTTCC
AGTTCAAAGTCAAAAGAGAGAACTTTTTGTAATATTCATGTCAGTCTAGTCCCTCAGCCAAGTTCAACAGGGGAACAGAA
GACTAAACCAACCCAGAATAGTGTTCGGGAACTTAGAGGGCTTGGGCTTTCCCCGGATCTGGTTGTGTGCAGGTGCTCAA
ATCCTTTGGACACATCAGTGAAAGAGAAAATATCAATGTTTTGCCACGTTGAACCAGAACAAGTGATCTGTGTCCATGAT
GTTTCATCCATCTACCGAGCCCCCCTGTTGTTAGAGGAGCAAGGGGTTGTAGATTATTTTCTTCGAAGACTTGACCTTCC
TATGGAGAGGCAGCCACGAAAAATGTTGATGAAGTGGAAAGAGATGGCTGACAGATATGATCGCTTGCTGGAAACCTGTT
CTATTGCCCTCGTGGGCAAATACACCAAGTTCTCAGACTCATATGCCTCTGTCATTAAAGCTCTGGAGCATTCTGCACTG
GCCATCAACCACAAATTGGAAATCAAGTACATAGATTCTACGGACTTGGAGTCGAGCACCTTACAAGAAGAGCCTGTACG
GTACCACGAAGCTTGGCAGAAACTCTGCAGTGCTCATGGAGTGCTGGTTCCAGGAGGGTTTGGTGTTTGAGGAACAGAAG
GAAAGATCCAAGCAATTGCCTGGGCTCGGAATCAGAGAAAGCCTTTTTTGGGTGTGTGCTTAGGAATGCATTTGGCAGTG
GTTGAATTTTCAAGAAATGTCCTGGGATGGCAAGATGCCAATTCTACAGAATTTGACCCTCAGACAAGTCATCCCGTGGT
CATAGACATGCCAGAACACAATCCTGGACAGATGGGCGGAACCATGAGGCTGGGCAAGAGGAGGACCCTGTTCCAGACCA
AGAACTCGGTCATG

Alignment

ORF - retro_chof_2469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.3 %
• Parental protein coverage: 75.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPHITDAIQEWVMRQALIPVDEDGLEPQVCVIELGGTVGDIESMPFIEAFRQFQFKVKRENF-CNIHVSL
          VPHITDAIQEWVMRQAL.PVDEDGLEPQVCVIELGGTVGDIESMPFIEAFRQFQFKVKRENF.CNIHVSL
Retrocopy VPHITDAIQEWVMRQALSPVDEDGLEPQVCVIELGGTVGDIESMPFIEAFRQFQFKVKRENF>CNIHVSL

Parental  VPQPSSTGEQKTKPTQNSVRELRGLGLSPDLVVCRCSNPLDTSVKEKISMFCHVEPEQVICVHDVSSIYR
          VPQPSSTGEQKTKPTQNSVRELRGLGLSPDLVVCRCSNPLDTSVKEKISMFCHVEPEQVICVHDVSSIYR
Retrocopy VPQPSSTGEQKTKPTQNSVRELRGLGLSPDLVVCRCSNPLDTSVKEKISMFCHVEPEQVICVHDVSSIYR

Parental  VPLLLEEQGVVDYFLRRLDLPIERQPRKMLMKWKEMADRYDRLLETCSIALVGKYTKFSDSYASVIKALE
          .PLLLEEQGVVDYFLRRLDLP.ERQPRKMLMKWKEMADRYDRLLETCSIALVGKYTKFSDSYASVIKALE
Retrocopy APLLLEEQGVVDYFLRRLDLPMERQPRKMLMKWKEMADRYDRLLETCSIALVGKYTKFSDSYASVIKALE

Parental  HSALAINHKLEIKYIDSTDLESSTLQEEPVRYHEAWQKLCSAHGVLVPGGFGVRGTEGKIQAIAWARNQR
          HSALAINHKLEIKYIDSTDLESSTLQEEPVRYHEAWQKLCSAHGVLVPGGFGV.GTEGKIQAIAWARNQR
Retrocopy HSALAINHKLEIKYIDSTDLESSTLQEEPVRYHEAWQKLCSAHGVLVPGGFGV*GTEGKIQAIAWARNQR

Parental  KPFLGVCLGMQLAVVEFSRNVLGWQDANSTEFDPQTSHPVVIDMPEHNPGQMGGTMRLGKRRTLFQTKNS
          KPFLGVCLGM.LAVVEFSRNVLGWQDANSTEFDPQTSHPVVIDMPEHNPGQMGGTMRLGKRRTLFQTKNS
Retrocopy KPFLGVCLGMHLAVVEFSRNVLGWQDANSTEFDPQTSHPVVIDMPEHNPGQMGGTMRLGKRRTLFQTKNS

Parental  VM
          VM
Retrocopy VM

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_2469 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005540	1 retrocopy	retro_chof_2469 ,
Cavia porcellus	ENSCPOG00000003389	1 retrocopy	retro_cpor_271,
Otolemur garnettii	ENSOGAG00000015398	1 retrocopy	retro_ogar_1936,