RetrogeneDB ID: retro_chof_2605

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_8977:1420..2073(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000013304
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013237
• Aliases: None
• Description: None

Sequence

>retro_chof_2605
GTCAAAGGTGGAGAAACAAGACTTAACACGGAGAAAGTACTTCAAGGACAAGGAATAAAAGAGCCTCTTTCAGAAACTGG
ATTTAAACAAGCAGCCACCAGGGGTATACATCTTAAAAATGTCAAGTTTACTCATGCTTTCTCTGGTGATCTCATGAGGA
CTAAGCAGTCCATGCATGGGACTTTGGAGAAAAGCAAATTTTGCAATAATATGACAGTAAAGTATGATTCGAGACTTCAA
GAAAGGAAATATTGGGTTGCAGAAGGTGAGGTGCTGACTGAGCTAAGGGCCTTGGTGAAAGTAGCTGGGGAAGAATGCCC
TACCTTCACCCCACCCAGAGGAGAGATGTTGGACCACATGAAAATGCATGGAAAAGACTTTTTTGAAAATCTTTGTCAAC
TGATCCTGGAAGAAGCAGGTCAAAAAAACAGTTCTCACAAGGTGCACCAGGCAACTCTCTGGAAACTTCTTTAGCAGAAA
TATTTCTTTTGTCAAAAACCTTGGATCCAAATTTAATTCAAATGGCAGTACTACGGGATTAGTAGACAGTGTCTTCGTGG
TGAGTCCATAGAGCTTATATGAGAAGCCTGTTTGATTATTTTCTGACTGACCTTAAGTGTTCCTTTCCAGCAACTGTGAG
CAAATCTGAGATT

Alignment

ORF - retro_chof_2605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.54 %
• Parental protein coverage: 80.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IRHGETRLNKEKVLQGQGIDEPLSETGFKQAAAVGIYLKNVKFSHAFSSDLTRTKQTMHGILEKSKLCNN
          ...GETRLN.EKVLQGQGI.EPLSETGFKQAA..GI.LKNVKF.HAFS.DL.RTKQ.MHG.LEKSK.CNN
Retrocopy VKGGETRLNTEKVLQGQGIKEPLSETGFKQAATRGIHLKNVKFTHAFSGDLMRTKQSMHGTLEKSKFCNN

Parental  MTVKYDSKLRERKYGVAEGKALTELRTLAKIAGEECPTFTPPGGETLDQVKMRGKVFFENLCQLILEEAD
          MTVKYDS.L.ERKY.VAEG..LTELR.L.K.AGEECPTFTPP.GE.LD..KM.GK.FFENLCQLILEEA.
Retrocopy MTVKYDSRLQERKYWVAEGEVLTELRALVKVAGEECPTFTPPRGEMLDHMKMHGKDFFENLCQLILEEAG

Parental  Q-KEQFSQGAPGNSLETSLAEIFPLA-KNLRSEFNSNGSTPGLAASVLVVS-HGAYMRSLFDYFLTDLKC
          Q.K.QFSQGAPGNSLETSLAEIF.L..KNL.S.FNSNGST.GL..SV.VVS.H.AYMRSLFDYFLTDLKC
Retrocopy Q<KKQFSQGAPGNSLETSLAEIFLLS<KNLGSKFNSNGSTTGLVDSVFVVS>HRAYMRSLFDYFLTDLKC

Parental  SLPATVSKSEI
          S.PATVSKSEI
Retrocopy SFPATVSKSEI

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_2605 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013237	2 retrocopies	retro_chof_2605 , retro_chof_792,
Mus musculus	ENSMUSG00000038028	1 retrocopy	retro_mmus_2365,
Tursiops truncatus	ENSTTRG00000016535	1 retrocopy	retro_ttru_1692,