RetrogeneDB ID: retro_chof_1765

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_379572:44..1064(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP43
• Ensembl ID: ENSCHOG00000009426
• Aliases: None
• Description: nucleoporin 43kDa [Source:HGNC Symbol;Acc:21182]

Sequence

>retro_chof_1765
GAAAATTATGTTTCACTGTGGTCTATTGGAGATTTTGGCAACTTGGACTCTAACGGAGGTTTTGGAGGAGACCATCAGTT
ATTGTGTGATATCAGACACCATGGTGATGTAATGGATTTGCAATTTTTAGACCAGGAAAGAATCGTAGCGGCTTCATCAA
CAGAATGTGTGACTAGTTTCCTTCACCATCAGAATAACCAGACACTGTCAGTCAACCAGCAGTGGACAACAGTGCACCAC
CGCACCGGGCCGGGCGGTCCCTCCTATAGCAGCTCCCCATGCACTGGGGTCATGTGCAACAACCCCGAGATCATCACAGT
CGGTGAAGATTGTAGGATAAATCTCTTCAGAGCTGATCACAGGGAAGCTGTGAGAACAATAGACACTGCAGATAGCAGTA
CACTACATGCTTCAACCTTCCTTCAAACTCCTGAGATTCTGACAGTAAATTCAATTGGACAGTTAAAAATATGGGATTTC
AGACAACAAGGAAATGAGCCTTCTCAGATATTATCACTGACTGGTGACCGAGTGCCACTCCACTGTGTTGACAGACATCC
CAACCAGCAGCATGTTGTAGCCACTGGTGGCCAGGATGGAATGCTGAGTATTTGGGATGTCAGACAAGGTTCTATGCCAG
TGTCTCTTCTGAAGGCTCATGAAGCTGAAATGTGGGAAGTTCACTTTCACCCGTCCAACCCAGATCATCTATTCACTTGT
TCTGAGGATGGATCCCTCTGGCATTGGGATGCCTCCACAGACAAACCTGAGAAATCATCACTCTTTCAACAAGGTGGAAG
AAGTAGTACTTTTTTGTCTCATAGCATAAGTAACCAGGCTAATGTCCACCATTCTCTACTAAGTTCCTGGCTCAGCACTG
ATCCTGCCAAAGACCGGATTGAAATCACAAGCTTGCTTCCCAGCAGGACTCTGTCAGTAAATAGTTTAGATGTTTTAGGT
CCTTGTCTAGTTTGTGGAACTGATGCAGAAGCAATTTATGTTACTAGACAACTTTTTTCA

Alignment

ORF - retro_chof_1765 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENYVSLWSFGDFGNFDSDGGFGGDHQLLCDIRHHGDVMDLQFLDHER-VAASSTGCVTIFLHHQNNQTLS
          ENYVSLWS.GDFGN.DS.GGFGGDHQLLCDIRHHGDVMDLQFLD.ER.VAASST.CVT.FLHHQNNQTLS
Retrocopy ENYVSLWSIGDFGNLDSNGGFGGDHQLLCDIRHHGDVMDLQFLDQERIVAASSTECVTSFLHHQNNQTLS

Parental  VNQQWTTAHHHTGLGSPSYSSAPCTGVVCNNPEIVTVGEDGRINLFRADHREAVRTIDNADSSTLHAVTF
          VNQQWTT.HH.TG.G.PSYSS.PCTGV.CNNPEI.TVGED.RINLFRADHREAVRTID.ADSSTLHA.TF
Retrocopy VNQQWTTVHHRTGPGGPSYSSSPCTGVMCNNPEIITVGEDCRINLFRADHREAVRTIDTADSSTLHASTF

Parental  LRTPEILTVNSIGQLKIWDFRQQGNEPSQILSLTGDRVPLHCVDRHPNQQHVVATGGQDGMLSIWDVRQG
          L.TPEILTVNSIGQLKIWDFRQQGNEPSQILSLTGDRVPLHCVDRHPNQQHVVATGGQDGMLSIWDVRQG
Retrocopy LQTPEILTVNSIGQLKIWDFRQQGNEPSQILSLTGDRVPLHCVDRHPNQQHVVATGGQDGMLSIWDVRQG

Parental  SMPVSLLKAHEAEMWEVHFHPSNPDHLFTCSEDGSLWHWDASTDKPEKSSLFQQGGRSSTFLSHSISNQA
          SMPVSLLKAHEAEMWEVHFHPSNPDHLFTCSEDGSLWHWDASTDKPEKSSLFQQGGRSSTFLSHSISNQA
Retrocopy SMPVSLLKAHEAEMWEVHFHPSNPDHLFTCSEDGSLWHWDASTDKPEKSSLFQQGGRSSTFLSHSISNQA

Parental  NVHHSLLSSWLSTDPAKDRIEITSLLPSRTLSVNSLDVLGPCLVCGTDAEAIYVTRQLFS
          NVHHSLLSSWLSTDPAKDRIEITSLLPSRTLSVNSLDVLGPCLVCGTDAEAIYVTRQLFS
Retrocopy NVHHSLLSSWLSTDPAKDRIEITSLLPSRTLSVNSLDVLGPCLVCGTDAEAIYVTRQLFS

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_1765 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009426	1 retrocopy	retro_chof_1765 ,
Cavia porcellus	ENSCPOG00000010815	1 retrocopy	retro_cpor_481,
Macaca mulatta	ENSMMUG00000009830	1 retrocopy	retro_mmul_1962,
Monodelphis domestica	ENSMODG00000016808	2 retrocopies	retro_mdom_199, retro_mdom_353,
Ictidomys tridecemlineatus	ENSSTOG00000013449	1 retrocopy	retro_itri_990,
Tarsius syrichta	ENSTSYG00000000944	1 retrocopy	retro_tsyr_267,