RetrogeneDB ID: retro_chof_2034

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_461235:232..619(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000459
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SYF2
• Ensembl ID: ENSCHOG00000005273
• Aliases: None
• Description: SYF2 homolog, RNA splicing factor (S. cerevisiae) [Source:HGNC Symbol;Acc:19824]

Sequence

>retro_chof_2034
AAAAGACTAAAGTTACCTGCAAATTGGGAAGCCAAAAAAGCTCGTTTGGAATGGGAAGTGCGGGAAGAAGAAAGGAAAAA
GGAATGTGCAGCAAAAGGGGAAGACTATGAGAAAGTTAAATTGCTAGAGATCAGTGCAGAAGATGCAGAAAGATGGGAGA
GGAAAAAAAAGAGGAAAAACCCTGATCTGGGATTTTCAGATTATGCTGCTGCCCAGTTACGCCAGTATCATCGGTTGACC
AAGCAGATCAAACCTGACATGGAAACGTATGAGAGACTGAGAGAAAAGCAGGGAGAAGAGTTTTTCCCAACATCCAACAG
TCTTATTCATGGAACACATGTGCCTTCCACTGAGGAAATTGATAGGATGGTCATAGATCTGGAAAAA

Alignment

ORF - retro_chof_2034 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.47 %
• Parental protein coverage: 78.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQLKLPANWEAKKARLEWELREEEKKKECAAKGEDYEKVKLLEISAEDAERWERKKRN--PDLGFSXXAA
          K.LKLPANWEAKKARLEWE.REEE.KKECAAKGEDYEKVKLLEISAEDAERWER......PDLGFS..AA
Retrocopy KRLKLPANWEAKKARLEWEVREEERKKECAAKGEDYEKVKLLEISAEDAERWERXXXXXXPDLGFSDYAA

Parental  AQLRQYHRLTKQIKPDMETYERLREKQGEEFFPTSNSLIHGTHVPSTEEIDRMVIDLEK
          AQLRQYHRLTKQIKPDMETYERLREKQGEEFFPTSNSLIHGTHVPSTEEIDRMVIDLEK
Retrocopy AQLRQYHRLTKQIKPDMETYERLREKQGEEFFPTSNSLIHGTHVPSTEEIDRMVIDLEK

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_2034 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010115	1 retrocopy	retro_amel_566,
Bos taurus	ENSBTAG00000001651	1 retrocopy	retro_btau_478,
Choloepus hoffmanni	ENSCHOG00000005273	1 retrocopy	retro_chof_2034 ,
Callithrix jacchus	ENSCJAG00000018559	1 retrocopy	retro_cjac_467,
Homo sapiens	ENSG00000117614	1 retrocopy	retro_hsap_4152,
Monodelphis domestica	ENSMODG00000013951	1 retrocopy	retro_mdom_899,
Oryctolagus cuniculus	ENSOCUG00000013050	1 retrocopy	retro_ocun_1522,
Sarcophilus harrisii	ENSSHAG00000007152	1 retrocopy	retro_shar_15,