RetrogeneDB ID: retro_chof_848

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_155258:3520..4402(+)
• 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_848
TGGAAGCTGACTGAGGCCGTGGCTGGAGGCTGGGTGCTGGTTGTTTGCACGGATGGCATCAGCTGCGAGCCCCTCAAGAA
CCTTGTGCTCACTGGCTTCTCCCACATCAACCTGATGGATCTGGATACTGTTGATGTCAGCAACCTCAACAAGCAGTTTT
TGTTTCAAAAGAAGCATGTTGGAAGATCAAAGGCACAGGGTGCCAAGGAAAGTGTACTGCAGTTTTATCCAAAAGCTAAT
CTCATAGCCGACCATGACAGCATCATGAACCCCAACTATAATGTGGAAATTTTTTGACAATTTATATTGGTTATGAATGC
TTTAGATAACAGAGCTGCCCACAAGTATGTAAATAGGATGTGTTTAGCAGCTGATGTCCCGCTTATGAGAGTGGAACTGC
TGGTTATCTTAGACAAGTAACTATTACTGAAAAGGGTATGACCGAGTGTTATGAATGTCATCCTAAACCAACCAGAGAAC
TTTTCCTGGCTGTACAATTCGTAACACACTTTCAGAACCTATTCATTGCATTGTTTGGGCAAAGTATTTGTTTAACCAAT
TGTTTTGGGAAGAAGATGCTGATCATGAAGTATCTCCTGACAGAGCTTATCCTGAAGCTGCCTCAGAACCAATGGAAGCT
GAAGCCAGAGCTAGAGCATCTAATGAAGATGGTGACAGTAAATGTATTTCCACTAAGGAATGAGAAAAATCAACTGGATA
TGATCCAGTTAAACTTTTTACCAAGCTTTTTAATGATGATATCAGGCATCTGTTGACAATGGCCATTCTTTGGCAGAAAA
GGAAACTCCAGTTCCATTGGACTGGGCTGAAGTACAAAGCCAAGGTGAAGAAATCAATGCAACAGATCAACAAAATGAAC
CT

Alignment

ORF - retro_chof_848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.54 %
• Parental protein coverage: 56.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WELA-AMGGGWVLVVGAGGIGCKLLKNLVCTGFSHISLIDLDASDVSNLNRQFLFQKKHIGRSKAQVAEE
          W.L..A..GGWVLVV...GI.C..LKNLV.TGFSHI.L.DLD..DVSNLN.QFLFQKKH.GRSKAQ.A.E
Retrocopy WKLTEAVAGGWVLVVCTDGISCEPLKNLVLTGFSHINLMDLDTVDVSNLNKQFLFQKKHVGRSKAQGAKE

Parental  SVLQFYPKAVFIAYHDSIMNPDYIVEFFREFILVMNALGNRAARNHVNRMCLAADVPLI-ESGTAGYLGQ
          SVLQFYPKA..IA.HDSIMNP.Y.VE.F..FILVMNAL.NRAA...VNRMCLAADVPL..ESGTAGYL.Q
Retrocopy SVLQFYPKANLIADHDSIMNPNYNVEIF*QFILVMNALDNRAAHKYVNRMCLAADVPLM<ESGTAGYLRQ

Parental  VTIIKKGVTECYECHPKPT-QRTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAA
          VTI..KG.TECYECHPKPT.QRTFPGCTIRNT.SEPIHCIVWAKYLFNQLF.EEDAD.EVSPDRA.PEAA
Retrocopy VTITEKGMTECYECHPKPT<QRTFPGCTIRNTLSEPIHCIVWAKYLFNQLFWEEDADHEVSPDRAYPEAA

Parental  WEPMEAEARARASNEDGDIKRISTKEWAKSTGYDPIKLFTKLFKDDIRYLLTMDKLWRKRK-PPVPLDWA
          .EPMEAEARARASNEDGD.K.ISTKE..KSTGYDP.KLFTKLF.DDIR.LLTM..LW.KRK..PVPLDWA
Retrocopy SEPMEAEARARASNEDGDSKCISTKE*EKSTGYDPVKLFTKLFNDDIRHLLTMAILWQKRK<TPVPLDWA

Parental  EVQSQGEETNASDQQNEP
          EVQSQGEE.NA.DQQNEP
Retrocopy EVQSQGEEINATDQQNEP

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_848 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,