RetrogeneDB ID: retro_chof_2349

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_67550:1254..2263(+)
• 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_2349
GTTCCAGAATATCTTAACTATGTAAGTGAATGTTTAGAAGAAGAAGGAGACCAAGTAATCACACATTTAGACCACAGTAC
ACAGAAATTACTGATTGTCTGCATGGAGAAACAGCTATTAGGAGAACATTTAACAGCAATTCTGCAGAAAGGTCTTGATC
ACTTACTCAATGAGCATAGAGTACCTGATCTCACACAGATGTACCAGTTGTTAAGTCGAGTAAAAGGTGGCCAGCAGATA
TTATTGCAGCACTGGAGTGAATACATCAAGAATTTTGGAATGACAATAGTTATCAATCCTGAAAAAGACAAAGATATGGT
GCAAGACCTACTATATTTTAAAGATAAAGTGGGCCACATCATAGAAGTGTGTTTTCAGAGAAATGAAAAATTTATCAACT
CAATGAAGGAGTCCTTTGAAACATTTATCAAGAATAGAGCAAATAAGCCTGCAGAATTGATTGCAAAACATGTTGATTCA
AAGTTAAGAGTGGGCAATAAAGAAGCAACAGATGATCAACTAGGGAGAATCCTTGACAAAATCATGATAATATTCACATT
TATACATGGTAAAGATGTTTTTGAAGCATTTTATTAAAAAGACTTGGCAAAAAGACTTCTTGTTGGAAAAAGTGCCTCAG
TAGGTGATGAAAAATCTGTTGTCAAAACTAAAATATGAATGTGGTGCTGCATTCACCAGCAAACTGGAAGGCATATTCAA
AGACATGGAACTTTTGAAAGACAGCATGGTTCATTTTAAGCAGTATATGCAGAATCAAAGTGATCCAGGATTTATAGATC
TAACAATAAATATACTTGCAATGGGATACTGGTTTACCTACACACCTATGGAAGTACATTTAACTCCAGAAATGATTAAA
CTTCAGGAAGTATTTAAAACATTTTATCTCAGAAAGCACAGTGGTTGAAAACTTCAGTGGCAAACTACTTTGGGACATGC
TGTTTTAAAAACTAAGTTTAAGGAAGGGAAGAAGGAGTTCCATGTGTCC

Alignment

ORF - retro_chof_2349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.39 %
• Parental protein coverage: 52.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPEYLNHVSKRLEEEGDRVITYLDHSTQKPLIACVEKQLLGEHLTAILQKGLDHLLDENRVPDLTQMYQL
          VPEYLN.VS..LEEEGD.VIT.LDHSTQK.LI.C.EKQLLGEHLTAILQKGLDHLL.E.RVPDLTQMYQL
Retrocopy VPEYLNYVSECLEEEGDQVITHLDHSTQKLLIVCMEKQLLGEHLTAILQKGLDHLLNEHRVPDLTQMYQL

Parental  FSRVKGGQQILLQHWSEYIKTFGTTIVINPEKDKDMVQDLLDFKDKVDHIIEVCFQKNEKFINLMKESFE
          .SRVKGGQQILLQHWSEYIK.FG.TIVINPEKDKDMVQDLL.FKDKV.HIIEVCFQ.NEKFIN.MKESFE
Retrocopy LSRVKGGQQILLQHWSEYIKNFGMTIVINPEKDKDMVQDLLYFKDKVGHIIEVCFQRNEKFINSMKESFE

Parental  TFINKRPNKPAELIAKHVDSKLRAGNKEATDEELERILDKIMIIFRFIHGKDVFEAFYKKDLAKRLLVGK
          TFI..R.NKPAELIAKHVDSKLR.GNKEATD..L.RILDKIMIIF.FIHGKDVFEAFY.KDLAKRLLVGK
Retrocopy TFIKNRANKPAELIAKHVDSKLRVGNKEATDDQLGRILDKIMIIFTFIHGKDVFEAFY*KDLAKRLLVGK

Parental  SASVDAEKSMLSKLK-HECGAAFTSKLEGMFKDMELSKDIMVHFKQYMQNQSDPGSIDLTVNILTMGYWP
          SASV..EKS...K.K..ECGAAFTSKLEG.FKDMEL.KD.MVHFKQYMQNQSDPG.IDLT.NIL.MGYW.
Retrocopy SASVGDEKSVV-KTK>YECGAAFTSKLEGIFKDMELLKDSMVHFKQYMQNQSDPGFIDLTINILAMGYWF

Parental  TYTPMEVHLTPEMIKLQEVFKTFYLGKHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVS
          TYTPMEVHLTPEMIKLQEVFKTFYL.KHSG.KLQWQTTLGHAVLK..FKEGKKEF.VS
Retrocopy TYTPMEVHLTPEMIKLQEVFKTFYLRKHSG*KLQWQTTLGHAVLKTKFKEGKKEFHVS

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_2349 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 ,