RetrogeneDB ID: retro_chof_2302

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_64605:8653..9002(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORC6
• Ensembl ID: ENSCHOG00000002944
• Aliases: None
• Description: origin recognition complex, subunit 6 [Source:HGNC Symbol;Acc:17151]

Sequence

>retro_chof_2302
AGTAGATCCCTTTTCACCACTGCTGCCTTACTTTTAGCATTCAAGATTCTGAAACTAAAAGTGGATAAAAATAAAATTGT
AGCCACATCCAATGTAAAAAAGACATCTTTGATAGACTCTGTAAACAATTAGAGAAGAATGGGCAGCAGATGGACATACA
GCCTAGAGATTTAGCTACTCTATCACAAAAGAAAAAGAAGACAGTGGTTGAACCCCCACAAAGAAAATAGAGAAAGTAGT
AGAGATCCCATATAAACCCCAGAAAGATGAAGGTCTGACACAGGATTATGAAGATCAGAAAAGGAAAATTTTGGAAAATG
CTGCTAAAGCATAAAAGGCTACAGCTGAG

Alignment

ORF - retro_chof_2302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.83 %
• Parental protein coverage: 88.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRPLFTTAALLSACRILKLKVDKNKMVITSGVKKA-IFDRLCKQLEKIGQQIDGQPRDLATPAPKKKKTV
          SR.LFTTAALL.A..ILKLKVDKNK.V.TS.VKK..IFDRLCKQLEK.GQQ.D.QPRDLAT...KKKKTV
Retrocopy SRSLFTTAALLLAFKILKLKVDKNKIVATSNVKKT<IFDRLCKQLEKNGQQMDIQPRDLATLSQKKKKTV

Parental  VEPT-TKEIEKVVEIPHKLQKDEDLTQDYEEWKRKILENAAKAQKATAE
          VEP..TK.IEKVVEIP.K.QKDE.LTQDYE..KRKILENAAKA.KATAE
Retrocopy VEPP<TKKIEKVVEIPYKPQKDEGLTQDYEDQKRKILENAAKA*KATAE

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_2302 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002944	1 retrocopy	retro_chof_2302 ,
Dasypus novemcinctus	ENSDNOG00000010859	1 retrocopy	retro_dnov_838,
Erinaceus europaeus	ENSEEUG00000012122	1 retrocopy	retro_eeur_489,
Otolemur garnettii	ENSOGAG00000000688	1 retrocopy	retro_ogar_1426,
Sarcophilus harrisii	ENSSHAG00000004207	2 retrocopies	retro_shar_211, retro_shar_759,
Tupaia belangeri	ENSTBEG00000000278	1 retrocopy	retro_tbel_3089,
Tarsius syrichta	ENSTSYG00000005205	2 retrocopies	retro_tsyr_1294, retro_tsyr_889,
Tursiops truncatus	ENSTTRG00000013294	1 retrocopy	retro_ttru_1528,