RetrogeneDB ID: retro_chof_1034

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_187601:2962..3811(+)
• 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_1034
TTTTGTTTCAAAAGAAGGCATATTGGAAGATCAAGGCACAAGGTTGCTGAGAAAGTGGTACTTCAGTTTATCCAAAAGCT
TTTTCATAGCCTACCATGACAGCATCATGAACCCCGACTATATGTGGAATTTTTAGAGAATTTATATTGGTTATGAATGC
TTTTAGGTAACAGAGCTGCCCGCAACCATGTAAATAGATGTGAACTTGCAGTTGATGTCCCTCTTATTGAGAGTGGAACT
GTTGGTTATCTTGGACAAGTAACTATTATTAAACTAGGTATGACTGAGTGTTATGAATGTCATCTTAAACCAACCCAGAG
AACTTTTCCTGGCTGTACAATTCATAACACAACCTTCAGAACCTATTCATTGCATTGTTTGGGCAAAGTATTTGTTTAAC
CAATTGTTTGGGGAAGAAGATGCTGATCAAGAAGTATCTCCTGATGGCACTGACCCTGAAGCTGCCTGGGAACCAATGGA
AGCTGAAACCAGAGCTAGAGCATCTAAGAAGATGGTGACATTAAATGTATTTCCACTAAGGAATAGGCTAAATCAACTGG
ATATGATCCAATTAAACTTTTTACCAAGCTTTTTAAAGATGATATCAGGTATCTGTTGACAATAGACAAACTTTGGTGGA
AAAGGAAACCACTAGTTCTGTTGGACTGGACTGGAGTACAAAGTCAAGGTGAAGAAACCATTGCATCAGATCAACAAAAT
GAACACCAGTTAGGTCTGAAATACCAGCAGGTTCTAGACATAAAGAACCATGCAAGTTTTTTTTTGAAGAGCATTGAGAC
TTTGAGAGTTCATTTAGCAGAAGAAGTGGATGGAGCTGAGGTCATGTGG

Alignment

ORF - retro_chof_1034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.13 %
• Parental protein coverage: 54.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  FLFQKKHIGRSKAQVAEESVLQF-YPKAV-FIAYHDSIMNPDYI-VEF-FREFILVMNA-LGNRAARNHV
          F.F...HIGRS...VAE..VLQF.YPKA..FIAYHDSIMNPDY..VEF.FREFILVMNA.LGNRAARNHV
Retrocopy FCFKRRHIGRSRHKVAEKVVLQF<YPKAF<FIAYHDSIMNPDYM<VEF<FREFILVMNA>LGNRAARNHV

Parental  NRMCLAADVPLIESGTAGYLGQVTIIKKGVTECYECHPKPTQRTFPGCTIRNT-PSEPIHCIVWAKYLFN
          NR..LA.DVPLIESGT.GYLGQVTIIK.G.TECYECH.KPTQRTFPGCTI.NT.PSEPIHCIVWAKYLFN
Retrocopy NRCELAVDVPLIESGTVGYLGQVTIIKLGMTECYECHLKPTQRTFPGCTIHNT>PSEPIHCIVWAKYLFN

Parental  QLFGEEDADQEVSPDRADPEAAWEPMEAEARARASN-EDGDIKRISTKEWAKSTGYDPIKLFTKLFKDDI
          QLFGEEDADQEVSPD..DPEAAWEPMEAE.RARAS..EDGDIK.ISTKE.AKSTGYDPIKLFTKLFKDDI
Retrocopy QLFGEEDADQEVSPDGTDPEAAWEPMEAETRARASK<EDGDIKCISTKE*AKSTGYDPIKLFTKLFKDDI

Parental  RYLLTMDKLWRKRKPPVPLDWAEVQSQGEETNASDQQNEPQLGLKDQQVLDVKSYASLFSKSIETLRVHL
          RYLLT.DKLW.KRKP.V.LDW..VQSQGEET.ASDQQNE.QLGLK.QQVLD.K..A....KSIETLRVHL
Retrocopy RYLLTIDKLWWKRKPLVLLDWTGVQSQGEETIASDQQNEHQLGLKYQQVLDIKNHAXXXXKSIETLRVHL

Parental  AEKGDGAELIW
          AE..DGAE..W
Retrocopy AEEVDGAEVMW

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_1034 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 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,