RetrogeneDB ID: retro_chof_2662

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_95249:1869..2467(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000013965
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHMP2B
• Ensembl ID: ENSCHOG00000006615
• Aliases: None
• Description: charged multivesicular body protein 2B [Source:HGNC Symbol;Acc:24537]

Sequence

>retro_chof_2662
GTAATAAAGGAACAGAATCGAGAGTTTTGAGGTACACGGAGGGCTGTAATCAGAGATTGAGCAGCTTTAGAGAAACAAGA
AAAACAGCTGGAATTAGAAATTAAGAAAATGGCCAAGACTGGTAACAAAGAAGCTTGCAGGGTTTTAGCACAACAGCTTG
TACATCTACGGAAACAGAAAACAAGTACTTTTGCTGTAAGTTCAAAAGTCACTTCTATGTCCACACAAACCAAAGTGATG
AATTCCCAGATGAAGATGGCTGGAGCAATGTCTACTACAGCAAAAACAATGCAGGCAGTCAACAAGAAGATGGATCCACA
AAAGACATTACAAACAATGCAGAATTTCCAGAAGGAAAATATGAAAATGGAAATGACCAAAGAAATGATCAGTGACAAAC
TTGATGACATCTTTGATGGCTCTGATGATGAAGAAGAAAGCCAGGATATTGTGAATCAAGTTCTTGATGAAATTAGAATT
GAAATCTCTGGAAAGATGGCCAAAACTCCATCCGCTGCCCAAAGCTTACCATCTGCCTCTACTCCAAAGGCTACAATCTC
CAATGAACGGGATTGAAAGGCAACTCAAAGCTTTAGGA

Alignment

ORF - retro_chof_2662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.0 %
• Parental protein coverage: 94.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VIKEQNRELRGTQRAIIRDRAALEKQEKQLELEIKKMAKIGNKEACRVLAKQLVHLRKQKTRTFAVSSKV
          VIKEQNRE..GT.RA.IRD.AALEKQEKQLELEIKKMAK.GNKEACRVLA.QLVHLRKQKT.TFAVSSKV
Retrocopy VIKEQNREF*GTRRAVIRD*AALEKQEKQLELEIKKMAKTGNKEACRVLAQQLVHLRKQKTSTFAVSSKV

Parental  TSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTMQNFQKENMKMEMTEEMINDTLDDIFDG
          TSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTMQNFQKENMKMEMT.EMI.D.LDDIFDG
Retrocopy TSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTMQNFQKENMKMEMTKEMISDKLDDIFDG

Parental  SDDEEESQDIVNQVLDEIGIEISGKMAKAPSAARSLPSASTSKATISDEE-IERQLKALG
          SDDEEESQDIVNQVLDEI.IEISGKMAK.PSAA.SLPSAST.KATIS.E..IERQLKALG
Retrocopy SDDEEESQDIVNQVLDEIRIEISGKMAKTPSAAQSLPSASTPKATISNER>IERQLKALG

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_2662 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006615	2 retrocopies	retro_chof_2662 , retro_chof_309,
Macropus eugenii	ENSMEUG00000012195	1 retrocopy	retro_meug_106,
Myotis lucifugus	ENSMLUG00000009052	1 retrocopy	retro_mluc_1557,
Monodelphis domestica	ENSMODG00000016939	2 retrocopies	retro_mdom_522, retro_mdom_605,
Ictidomys tridecemlineatus	ENSSTOG00000011456	1 retrocopy	retro_itri_1036,