RetrogeneDB ID: retro_chof_2031

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_46035:8582..10090(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CUL4A
• Ensembl ID: ENSCHOG00000011498
• Aliases: None
• Description: cullin 4A [Source:HGNC Symbol;Acc:2554]

Sequence

>retro_chof_2031
GTTCCAGAATATCTTAACCATGTAAGTAAACGTTTAGAAGAAGGAGACCGAGTAATCACCTATTTAGCCCACAGTACACA
GAAACCACTGATTGCCTGTGTGGGAAAACAGCTATTAGGAGAACATTTAACAGCAATTCTGCAGAAAGGGCTTGATCACT
TACTCGATGAGAATAGAGTACCTGATCTCACACAGATGTACCAGTTGTTCAGTCGAGTAAAAGGCGGCCAGCAGATATTA
CTGCAGCACTGGAGTGAATACATAAAGACTTTTGGAACAACAATAGTTATCAATCCTGAAAAAGATAAAGATATGGTGCA
AGACCTGCTAGATTTTAAAGATAAAGTGTACCACATCATAGAAGTGTGCTTTCAGAAAAATGAAAAATTTATCAACTTGA
TGAAGGAATCCTTTGAAACATTTATCAACGAGAGAACAAATAAGCCTGCAGAACTGATTGCAAAGCATGTTGATTCAAAG
TTAAGAGCGGGTAATAAAGAAGCAACTGATGAAGAACTAGAAAGAATCCTTGACAAAATCATGATAATATTCAGGTTTAT
TCATGGTAAAGATGTTTTTGAAGCATTTTATAAAAAAGACTTGGCAAAAAGACTTCTTGTTGGAAAAAGTGCCTCAATAG
ATGCTGAAAAGTCTGTGTTGTCAAAACTAAAACATGAATGTGGTGCTGCATTCACCAGCAAACTGGAAGGTATGTTCAAG
GACATGGAACTTTCAAAAGACATCATGGTTCATTTTAAGCAGTATATGCAGAATCGAAGTGATCCAGGATCTATCGCTCT
AACAGTAAGTATACTTACAATGGGATACTGGCCAACATACACACCTATGGAAGTACATTTAACTCCAGAAATGATTAAAC
TTCAGGAAGTATTTAAAACATTTTATCTTGGAAAGCACAGTGGTCGAAAACTTCAGTGGCAAACAACTTTGGGACATGCT
GCTTTAAAAGCTGAGTTTAAAGAAGGAACGAAGGAGTTTCAGGTGTCTCTTTTCCAAACGTTAGTGCTTCTCATGTTTAA
CAAAGAAGATGAATTCAGTTTTGAAGAAATAAAAATGGCTACTGGTATAGAGAATAGTGAATTGCGAAGAACATTACAAT
CACTGGCTTGTGGTAAAGCACGTGTGCTGATTAAAAGTTCAAAAGTAAAGGATGTTGAAGATGGAGACAAATTCATTTTT
AATGGAGAGTTCAAGCACAAGTTGTTTAGAATAAAGATCAGTCAAATTCAGATGAAAGAAACTGTTGAGGAAAAAGTTAG
CACCAGGGAAAGAGTGTTTCAGGATAGACAATACCAGATTGATGCTCTATATTAAGAATAATGAAAATGAGAAATACTCT
TGGTCATAATCTTCTAGTCTCTGAATTATATAATCAGCTGAAATTTCCAGTAAAGCCTGGAGATCTAAAAAAGAGAATTG
AATCTCTTATAGAAAGAGCCTATATGGAGAGAGAGAAAGACAATCCGAATCAGTACCACTACGTGGCA

Alignment

ORF - retro_chof_2031 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.46 %
• Parental protein coverage: 79.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPEYLNHVSKRLEEEGDRVITYLDHSTQKPLIACVEKQLLGEHLTAILQKGLDHLLDENRVPDLTQMYQL
          VPEYLNHVSKRLEE.GDRVITYL.HSTQKPLIACV.KQLLGEHLTAILQKGLDHLLDENRVPDLTQMYQL
Retrocopy VPEYLNHVSKRLEE-GDRVITYLAHSTQKPLIACVGKQLLGEHLTAILQKGLDHLLDENRVPDLTQMYQL

Parental  FSRVKGGQQILLQHWSEYIKTFGTTIVINPEKDKDMVQDLLDFKDKVDHIIEVCFQKNEKFINLMKESFE
          FSRVKGGQQILLQHWSEYIKTFGTTIVINPEKDKDMVQDLLDFKDKV.HIIEVCFQKNEKFINLMKESFE
Retrocopy FSRVKGGQQILLQHWSEYIKTFGTTIVINPEKDKDMVQDLLDFKDKVYHIIEVCFQKNEKFINLMKESFE

Parental  TFINKRPNKPAELIAKHVDSKLRAGNKEATDEELERILDKIMIIFRFIHGKDVFEAFYKKDLAKRLLVGK
          TFIN.R.NKPAELIAKHVDSKLRAGNKEATDEELERILDKIMIIFRFIHGKDVFEAFYKKDLAKRLLVGK
Retrocopy TFINERTNKPAELIAKHVDSKLRAGNKEATDEELERILDKIMIIFRFIHGKDVFEAFYKKDLAKRLLVGK

Parental  SASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMVHFKQYMQNQSDPGSIDLTVNILTMGYWPT
          SAS.DAEKS.LSKLKHECGAAFTSKLEGMFKDMELSKDIMVHFKQYMQN.SDPGSI.LTV.ILTMGYWPT
Retrocopy SASIDAEKSVLSKLKHECGAAFTSKLEGMFKDMELSKDIMVHFKQYMQNRSDPGSIALTVSILTMGYWPT

Parental  YTPMEVHLTPEMIKLQEVFKTFYLGKHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTLVLLMFNEG
          YTPMEVHLTPEMIKLQEVFKTFYLGKHSGRKLQWQTTLGHA.LKAEFKEG.KEFQVSLFQTLVLLMFN..
Retrocopy YTPMEVHLTPEMIKLQEVFKTFYLGKHSGRKLQWQTTLGHAALKAEFKEGTKEFQVSLFQTLVLLMFNKE

Parental  DEFSFEEIKMATGIEDSELRRTLQSLACGKARVLIKSPKGKDVEDGDKFIFNGEFKHKLFRIKINQIQMK
          DEFSFEEIKMATGIE.SELRRTLQSLACGKARVLIKS.K.KDVEDGDKFIFNGEFKHKLFRIKI.QIQMK
Retrocopy DEFSFEEIKMATGIENSELRRTLQSLACGKARVLIKSSKVKDVEDGDKFIFNGEFKHKLFRIKISQIQMK

Parental  ETVEEQVSTTERVFQDRQYQIDA-AIVRIMKMRKTLGHNLLVSELYNQLKFPVKPGDLKKRIESLIDRDY
          ETVEE.VST.ERVFQDRQYQIDA..I.RIMKMR.TLGHNLLVSELYNQLKFPVKPGDLKKRIESLI.R.Y
Retrocopy ETVEEKVSTRERVFQDRQYQIDA<SILRIMKMRNTLGHNLLVSELYNQLKFPVKPGDLKKRIESLIERAY

Parental  MERDKDNPNQYHYVA
          MER.KDNPNQYHYVA
Retrocopy MEREKDNPNQYHYVA

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_2031 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011498	2 retrocopies	retro_chof_2031 , retro_chof_2349,