RetrogeneDB ID: retro_chof_541

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_11940:21446..22069(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBAC1
• Ensembl ID: ENSCHOG00000011350
• Aliases: None
• Description: UBA domain containing 1 [Source:HGNC Symbol;Acc:30221]

Sequence

>retro_chof_541
CTGGAAGACCTCAAAAGTGTGCACATGTAAGTAATACACGCTGCTTTAGAGAGGTTGCTGAGTGATGCCAAACCCATCTT
AGAAGATAACTTTCAGGATCAAGATATCTTATTGCTGATTTAAAAAAAAAAAGGGGGGGGCACCCCAGTTCTAAGGCAGA
TGATATCTCAGCAGAAGAAAAGAAGAAACAAGACCGGAAAGCTCCAGATAGAGATCCTATATTCTGAGCCACAGCCAACC
TACTGTCATGCAGTGTGGACCAGGCCATGGCACAGCCCAACATGAGAGACTTCCAGACAGAACTCCAGAAAATTTTGGTA
TCTTTCCTCAAGGTGCCACGAAACTTAGCACTGAACCCTGGTGCAGCTGAATTATTTCAGAAGGCAAATTCTATGTTAGA
TAAAGAAGAGGAAGAGCAAGTGGATGACACTTTGCACTGGCTCACAGAGATGGTCTTCCCAGAGAGGAAAGCCCTGAAGT
CCCTTTGGCTGAACCACATGTCAGTAATTCAGGCCATGGAGTGAACTGAGCCTGCAGAAGACCCTATCATAGACACGCTT
ATTCCAGGCCAAGCCTCCCCAGAAGCCTAGGGGGCCATGGTGGCCTCCCTTATGGCTGCTGCT

Alignment

ORF - retro_chof_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.62 %
• Parental protein coverage: 65.02 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LEDPKSVTHHKLIHAASERVLSDTKTILEENI--QDRDVLLLIKKRAPSPV-PKMADVSAEEQKKQDQKA
          LED.KSV.H...IHAA.ER.LSD.K.ILE.N...QD...L.........PV..K..D.SAEE.KKQD.KA
Retrocopy LEDLKSV-HM*VIHAALERLLSDAKPILEDNFQDQDILLLIXXXXGGGTPV<SKADDISAEEKKKQDRKA

Parental  PDRDAIFQATANLPPCSMDREVAQPSMRDFQTELRKILVSLIEVAQKLLALNPDAVELFKKANAMLDEDE
          PDRD.IF.ATANL..CS.D...AQP.MRDFQTEL.KILVS...V....LALNP.A.ELF.KAN.MLD..E
Retrocopy PDRDPIF*ATANLLSCSVDQAMAQPNMRDFQTELQKILVSFLKVPRN-LALNPGAAELFQKANSMLDKEE

Parental  EAHVDEAALRQLTEMGFPESRAVKALRLSHMSVTQAMEWLIEHAEDPTIDTPLPGHATPDVPGAAVASSD
          E..VD...L..LTEM.FPE..A.K.L.L.HMSV.QAME...E.AEDP.IDT..PG.A.P...GA.VAS..
Retrocopy EEQVDD-TLHWLTEMVFPERKALKSLWLNHMSVIQAME-*TEPAEDPIIDTLIPGQASPEA*GAMVASLM

Parental  AAS
          AA.
Retrocopy AAA

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_541 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011350	2 retrocopies	retro_chof_2095, retro_chof_541 ,