RetrogeneDB ID: retro_chof_879

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_160435:1628..2267(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDFY2
• Ensembl ID: ENSCHOG00000010470
• Aliases: None
• Description: WD repeat and FYVE domain containing 2 [Source:HGNC Symbol;Acc:20482]

Sequence

>retro_chof_879
GACAACTGTACCCTGGTCACAACATTCAGAAGACATACAGCCACCTGCACCCAAGCCACATCTGGGCCTGGTGGGGTGAC
TGCTGTCTGTTGGGACCTCATCCAGCCAGCATTGTTCCCAGACAGTTTAGGCCACTCTGTTATCATGCAGGATGTCAGTG
GGAGAAAAGGAACAGCCATCGAGCTCCAAGGACAGAATGATAAAGTCCGCACATTGTTGTCTTTGCCAGCACATACAGCA
GCTCATCTCATGGGGCGAGGACAGTGGGACTTTAGTCTTGAAAAAAGACATGGAGAGGCAGGAGATCCCTGAATATTTGG
ACAGTGATTCCTGTCAAAAGTGTGATCAGACTCTCTTCTGGAACTTCAAGCACATGTGAGACAGTAAGAAAACTGGCCTA
AGACGGCACAACTGCCACAAGAGTGGGAAGGCTGTGTGCGGCAAGCATAGCTCCAAGCAGTCCTCCATCCTGCTGATGGG
CTTCTAGTTTGAAGTGAGGGTCTGTGACAGCTGCCACGAGGCTGTCACAGATAAAGAACGTGCACCTCCAGCTACCTCTC
ATGACAGTAAACATAACATTGAACATGTGCACTTTAATGCAATCAGAGAGTGGTTACTGACTCTGGAACTGAGAATGTT

Alignment

ORF - retro_chof_879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.76 %
• Parental protein coverage: 55.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DHSGQVTILKLEQDSCTLVTAFRGHTGGVTALCWDPAQRVLFSGSSDHSVIMWDIGGRKGTAIELQGHND
          D....VT........CT..T......GGVTA.CWD..Q..LF..S..HSVIM.D..GRKGTAIELQG.ND
Retrocopy DNCTLVTTFRRHTATCTQATS---GPGGVTAVCWDLIQPALFPDSLGHSVIMQDVSGRKGTAIELQGQND

Parental  RVQAL-SYAQHTRQLISCGGDGGIVVWNMDVERQETPEWLDSDSCQKCDQPFFWNFKQMWDSKKIGLRQH
          .V..L....QH..QLIS.G.D.G..V...D.ERQE.PE.LDSDSCQKCDQ..FWNFK.M.DSKK.GLR.H
Retrocopy KVRTL>CLCQHIQQLISWGEDSGTLVLKKDMERQEIPEYLDSDSCQKCDQTLFWNFKHM*DSKKTGLRRH

Parental  HCRKCGKAVCGKCSSKRSCIPLMGFEFEVRVCDSCHEAITDEERAPTATFHDSKHNIVHVHFDATRGRLL
          .C.K.GKAVCGK.SSK.S.I.LMGF.FEVRVCDSCHEA.TD.ERAP.AT.HDSKHNI.HVHF.A.R..LL
Retrocopy NCHKSGKAVCGKHSSKQSSILLMGF*FEVRVCDSCHEAVTDKERAPPATSHDSKHNIEHVHFNAIREWLL

Parental  T-SGTDKV
          T.SGT..V
Retrocopy T<SGTENV

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_879 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010470	1 retrocopy	retro_chof_879 ,