RetrogeneDB ID: retro_chof_33

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_84945:6508..7387(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000922
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCYT1A
• Ensembl ID: ENSCHOG00000010073
• Aliases: None
• Description: phosphate cytidylyltransferase 1, choline, alpha [Source:HGNC Symbol;Acc:8754]

Sequence

>retro_chof_33
GACCAGCCTGTGAGAGTTTATGCAGATGGAATATTTGACTTATTTCACTCTGGTCATGCCCGGGCTCTGATGCAAGCAAA
GAACCTTTTCCCTAATACATATCTCATTGTGGGAGTCTGCAGTGATGAGCTGACGCACAACTTCAAAGGTTTCACGGTGA
TGAATGAAAATGAGCGCTACGATGCAGTGCAGCATTGCCGCTATGTGGATGAAGTGGTGAGGAATGCCCCCTGGACCCTG
ACACCCGAGTTCCTGGCAGAACACCGGATTGATTTTGTAGCCCATGATGACATCCCTTATTCTTCTTCTGGGAGTGATGA
TGTTTATAAGCACATCAAGGAAGCAGGCATGTTTGCTCCAACACAGAGGACAGAAGGTATCTCCACATCAGACATCATCA
CCCGAATTGTCCGGGACTATGATGTGTATGCGAGACGAAACCTACAGAGAGGCTACACAGCTAAGGAGCTCAATGTCAGC
TTTATCAATGAGAAGAAATACCATTTGCAGGAGCGGGTTGACAAAGTAAAGAAGAAAGTGAAAGACGTGGAAGAAAGGTC
AAAAGAATTTGTTCAGAATGTAGAGGAAAAAAGCATTGACCTCATTCAAAAATGGGAGGAGAAATCCCGAGAATTCATTG
GAAGTTTCCTGGAAATGTTTGGTCCTGAAGGAGCACTGAAACATATGCTGAAAGGAAAAGGCCGGATGCTGCAGGCCATC
AGTCCAAAGCAGAGTCCCAGCAGCAGCCCTACTCGTGAACGTTCCCCTTCCCCTTTTCGATGGCCCTTCTCTGGCAAGAC
TTCCCCACCTTCCTCTCCAGCAAACCTCTCCAGGCACAAGGCTGCAGCCTATGATATCAGTGAGGATGAAGAGGACTAA

Alignment

ORF - retro_chof_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.29 %
• Parental protein coverage: 80.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRPVRVYADGIFDLFHSGHARALMQAKNLFPNTYLIVGVCSDELTHNFKGFTVMNENERYDAVQHCRYVD
          D.PVRVYADGIFDLFHSGHARALMQAKNLFPNTYLIVGVCSDELTHNFKGFTVMNENERYDAVQHCRYVD
Retrocopy DQPVRVYADGIFDLFHSGHARALMQAKNLFPNTYLIVGVCSDELTHNFKGFTVMNENERYDAVQHCRYVD

Parental  EVVRNAPWTLTPEFLAEHRIDFVAHDDIPYSSAGSDDVYKHIKEAGMFAPTQRTEGISTSDIITRIVRDY
          EVVRNAPWTLTPEFLAEHRIDFVAHDDIPYSS.GSDDVYKHIKEAGMFAPTQRTEGISTSDIITRIVRDY
Retrocopy EVVRNAPWTLTPEFLAEHRIDFVAHDDIPYSSSGSDDVYKHIKEAGMFAPTQRTEGISTSDIITRIVRDY

Parental  DVYARRNLQRGYTAKELNVSFINEKKYHLQERVDKVKKKVKDVEERSKEFVQKVEEKSIDLIQKWEEKSR
          DVYARRNLQRGYTAKELNVSFINEKKYHLQERVDKVKKKVKDVEERSKEFVQ.VEEKSIDLIQKWEEKSR
Retrocopy DVYARRNLQRGYTAKELNVSFINEKKYHLQERVDKVKKKVKDVEERSKEFVQNVEEKSIDLIQKWEEKSR

Parental  EFIGSFLEMFGPEGALKHMLKEGKGRMLQAISPKQSPSSSPTHERSPSPFRWPFSGKTSPPSSPANLSRH
          EFIGSFLEMFGPEGALKHMLK.GKGRMLQAISPKQSPSSSPT.ERSPSPFRWPFSGKTSPPSSPANLSRH
Retrocopy EFIGSFLEMFGPEGALKHMLK-GKGRMLQAISPKQSPSSSPTRERSPSPFRWPFSGKTSPPSSPANLSRH

Parental  KAAAYDISEDEED
          KAAAYDISEDEED
Retrocopy KAAAYDISEDEED

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_33 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010073	1 retrocopy	retro_chof_33 ,
Monodelphis domestica	ENSMODG00000018432	1 retrocopy	retro_mdom_1643,