RetrogeneDB ID: retro_chof_548

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_120296:3276..4079(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA2
• Ensembl ID: ENSCHOG00000011975
• Aliases: None
• Description: ubiquitin-like modifier activating enzyme 2 [Source:HGNC Symbol;Acc:30661]

Sequence

>retro_chof_548
AGCCCCGACTATAATGTGAAATTTTTTCGACTCTTTATATTGGTTATGAATGCTTTAGAAAACAGAGCTGCCCACAATCA
TGTAAATAGGATGTGTCTAGCAGCTGATTTCCCTCTTATTGAGAGTGGACCTGTCACTTATCTTGGACAAGTAACTATTA
TTAAAAAGGGTGTGACTGACTATTATGAATCTCATCCTAAACCAACCCAGAGAACTTTTCCTGGCTGTTCAATTCGTAAC
ACACCTTCAGAACCTATTCATTGCATTGTTTGAGCGAAGTATTTGTTCAAACAATTGTCTGGGGAAGAAGATGCTGATCA
AGAAGCATCTCCTGGCAGAGCTGACCCTGAAGCTGCCTGGGAACCATTGGAAGCTGAAGCCAGAGCTAGAGCATCTAATG
AAGATGGTGACAGTAAATGTATTTCCACTAAGGAATGAGAAAAATCAACTGGATATGATCCAGTTAAACTTTTTACCAAG
CTTTTTAAAGATGATATCAGGTATCTGTTGACAATGGACAAACTTTGGCGGAAAAGGAAACCTCCAGTTCTGTTGGACTG
AGCTGAAGTACAAAGTCAAGGTGAAGAAACCAATTCATCAGATCAATAAAATGAACCCCAGTTAGGTCTGAAAGATGAGC
AGGTTCTAGATGTATGGAGCTATGCAAGTCTTTTTTCAAAGAACATTGAGACTTTGAGAGTTCATTTAGCAGAAAAAGGG
GATGGAGCTGAGCTCATATGGGACAAGGATGACTCATCTGCAATGGATTTTGTCACTTTGCTGCAAACTTCAGGATGCAC
ATT

Alignment

ORF - retro_chof_548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.25 %
• Parental protein coverage: 51.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPDYIVEFFREFILVMNALGNRAARNHVNRMCLAADVPLIESGTAGYLGQVTIIKKGVTECYECHPKPTQ
          .PDY.V.FFR.FILVMNAL.NRAA.NHVNRMCLAAD.PLIESG...YLGQVTIIKKGVT..YE.HPKPTQ
Retrocopy SPDYNVKFFRLFILVMNALENRAAHNHVNRMCLAADFPLIESGPVTYLGQVTIIKKGVTDYYESHPKPTQ

Parental  RTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPMEAEARARASNEDGDIKR
          RTFPGC.IRNTPSEPIHCIV.AKYLF.QL.GEEDADQE.SP.RADPEAAWEP.EAEARARASNEDGD.K.
Retrocopy RTFPGCSIRNTPSEPIHCIV*AKYLFKQLSGEEDADQEASPGRADPEAAWEPLEAEARARASNEDGDSKC

Parental  ISTKEWAKSTGYDPIKLFTKLFKDDIRYLLTMDKLWRKRKPPVPLDWAEVQSQGEETNASDQQNEPQLGL
          ISTKE..KSTGYDP.KLFTKLFKDDIRYLLTMDKLWRKRKPPV.LD.AEVQSQGEETN.SDQ.NEPQLGL
Retrocopy ISTKE*EKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVLLD*AEVQSQGEETNSSDQ*NEPQLGL

Parental  KDQQVLDVKSYASLFSKSIETLRVHLAEKGDGAELIWDKDDPSAMDFVT-SAANL-MHI
          KD.QVLDV.SYASLFSK.IETLRVHLAEKGDGAELIWDKDD.SAMDFVT..AAN..MHI
Retrocopy KDEQVLDVWSYASLFSKNIETLRVHLAEKGDGAELIWDKDDSSAMDFVT<FAANFRMHI

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_548 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011975	3 retrocopies	retro_chof_1034, retro_chof_548 , retro_chof_848,
Myotis lucifugus	ENSMLUG00000003047	1 retrocopy	retro_mluc_286,
Monodelphis domestica	ENSMODG00000011934	1 retrocopy	retro_mdom_1509,
Pongo abelii	ENSPPYG00000009837	1 retrocopy	retro_pabe_304,
Rattus norvegicus	ENSRNOG00000021113	1 retrocopy	retro_rnor_939,
Sus scrofa	ENSSSCG00000002876	1 retrocopy	retro_sscr_941,