RetrogeneDB ID: retro_chof_490

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_113885:2089..2924(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AQP10
• Ensembl ID: ENSCHOG00000012951
• Aliases: None
• Description: aquaporin 10 [Source:HGNC Symbol;Acc:16029]

Sequence

>retro_chof_490
ATGGCCCATACTCTGTGCCTGGCTGCAGTCAGGGACCAGTTCTGGATTCAGAGCCTCTTGGCCTGACAGTGCCTGGCAGA
GTTTCTGGGTGTGTTGTGGTCCTGCCCCTCACTCAGGGAGCTGTAGCCCAGGCTGTCACCAGAGAAGAAACAAAGGCAAC
GTCTTCACCATGTTTCTGGCTGGCTCTCTGGCCATGATGGTAACCATCTACATGGATGGCAATGTCTCAGGGTTTGCCAA
CCTGAATCCAGCCTTTTCCCTGGCCATATGTCTCCTGGGCTGCCTCCCCTGGGCCAAAATCCCCATTTACACCTTGGTGC
AGCTGCTATCTGCTTTTGTGCCTCAGGAGCCACCATCTATGTCCTATGATGCCCTACAGAACTATACAAGTGGGAACCTG
AGAGTGTCTGGCCCCAAGGAGACAGATTCTGTCTTTGCTACCTACCCTGCCCCCTATCTGTCCCTGAACAATGGCTTTGT
GGATCAGGTTCTGGGCACTGGGATCCTGACTGTGAGGATTTTGGCCATCCTGGACACCTGGAACAAAGAAGCGCCTTCAG
GTCTGGAGGCTGTGGCAGTGGGGCTGCTGATCCCAGTCACTGGGCCATCCATGGGTGCCAACTGTGGGTTCCAGCTGAAC
CCTGCCTGATCTGGGCCCCCAGCTTTTTACCTGTGTAGCTGGCTGGGGCTCTGAAGTCTTCAGTGCTGGTCATTGCTGGT
GGAGGGTGCCTGTGATAGCCCCCTGGTGGGTACCATGCTAGGCACAGCCACATACCAGCTGCTGCTCACTCTGCACCACC
CTGAGGACTTGGAGCAAACTCAGGATCTCAGACTT

Alignment

ORF - retro_chof_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.53 %
• Parental protein coverage: 93.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAHTLSLAAVRDRFRIRSLLARQCLAEVLGVF-VLMLLTQGAVAQAVTSGETK-GNFFTMFLAGSLAVTI
          MAHTL.LAAVRD.F.I.SLLA.QCLAE.LGV..V...LTQGAVAQAVT..ETK.GN.FTMFLAGSLA...
Retrocopy MAHTLCLAAVRDQFWIQSLLA*QCLAEFLGVL<VVLPLTQGAVAQAVTREETK<GNVFTMFLAGSLAMMV

Parental  AIYVGGNVSG-AHLNPAFSLAMCLLGRLPWVKLPIYILVQLLSAFCASGATYALYYDAIQNYTGGNLTVS
          .IY..GNVSG.A.LNPAFSLA.CLLG.LPW.K.PIY.LVQLLSAF..........YDA.QNYT.GNL.VS
Retrocopy TIYMDGNVSGFANLNPAFSLAICLLGCLPWAKIPIYTLVQLLSAFVPQEPP-SMSYDALQNYTSGNLRVS

Parental  GPKETASIFATYPAPYLSLNNGILDQXXXXXXXIVGILAILDTRNKGVPAGLEPVAVGLLILVIGLSMGA
          GPKET.S.FATYPAPYLSLNNG..DQ........V.ILAILDT.NK..P.GLE.VAVGLLI.V.G.SMGA
Retrocopy GPKETDSVFATYPAPYLSLNNGFVDQVLGTGILTVRILAILDTWNKEAPSGLEAVAVGLLIPVTGPSMGA

Parental  NCGFPINPARDLGP-RLFTYIAGWGSEVFSAGNGWWWVPVVA-PLVGAMLGTAVYQLMVALHHPEDLEPA
          NCGF..NPA...GP..LFT..AGWGSEVFSAG..WW.VPV.A.PLVG.MLGTA.YQL...LHHPEDLE..
Retrocopy NCGFQLNPA*S-GP>QLFTCVAGWGSEVFSAGHCWWRVPVIA<PLVGTMLGTATYQLLLTLHHPEDLEQT

Parental  QDLGL
          QDL.L
Retrocopy QDLRL

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_490 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	ENSCHOG00000012951	2 retrocopies	retro_chof_2573, retro_chof_490 ,