RetrogeneDB ID: retro_chof_1535

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_31684:5046..6387(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT11
• Ensembl ID: ENSCHOG00000001121
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11) [Source:HGNC Symbol;Acc:19875]

Sequence

>retro_chof_1535
TTCAGTGAAGTGACTCAGCCACTTAAGAATGTGCCCATCAAGGGGTCTGGGCCCCATGGACCAGTCCCCAAATAGTTCTA
ACTTCACTTTACTCAAGGTCAAAGTCAAGTACTAGAGCCACTGTTCAAAGCAAACAAGACTGGTGACATGATAGATAATC
AAAATGATGATCCAGGAAAAGACAGCATGAAATTCTCCCCTGAATTGGATATGATTTTAAATGAACATTATCAGGAGATG
AGAGACTTGAGCTATCAGAAACATGCTTTTAATATGCTTATTAACCGCTTGGGCTACCATAGAAATGTGTCAGATACAAG
GAATGCAGTATGTAAAGAAAAGTCTTACCCAACTGATCTTCTAGTTGCTAGCATTGTTTGTTTCTATGATGAAGTTTCTC
TGCATTGTTCTGGATAGTGCACAGTGTCATAGATCAGACTCTGGCACATCTTCTTCATGAAATTATTCTAGTGGACAATG
ATAGTGATTTTGATTATTTGAAAGGAGAACTAGATGAATATATCCAAAACTGCCTCCCTGGAAAAACTAAAGTAATAAGA
AATACGAAGCATGAGGGATTGATTCAAAAAGAATGATTGGAGCAGCACGTGCCACAAAAGAAGTTCTTGTATTCCTAGAT
AACCACTGTTAAGTGAATGAAGTCTGACTATAGCCCTTGCTGGCTGCAATCCATGAAGACCATTAAACTGTGGTCTGTGT
GGTGATTGATATCATCGTGCTGATACACTCAGTTACAGCTCATCTTCTATTGTATGAGAAGGATTCAAATGGAGACTACA
CTTTAAATGGGATCTTGTTCCTCTTTCTGAGTTAGAAGGACCAGAAGAAGCAACTGCACCAATAAAGTCACCTACAGTGG
CTGGAGGATTGTTTGCCATGAACAGACAATATTTCAATGAACTTGGACAGTATGACAGTGGCATGGATATTTGGGGAGGA
GAAAACTTGGAAATATCATTTTGGATCTGGATGTATGAAGGTAAGCTCTTCATCCCTTCCTCTAGAGTAGGACACATTTT
CCAGAAAAGATGACCATATGGATTTCCTGAGGGCCAGGACACAATGACACACAACTCTTTGAGGCTGGCACATGTATGGT
TGGATGAATATAAGGAACAGTATTTTTCCTTAAGACCTGCTCTGAAAACCAAAAGCTATGGAAATATTAGTGAGTGTGTT
GATTTGAGAAAGAAGTTGGGTTGTAAATCATTTAAATGGTATTTGGATAATATATACCCACAGATACAGATATCTGGGCC
CAATGCTGAACCACAGCAATGCATTTTTATTAATAGAAGGCCAAAATGCCCCAAAATCCTT

Alignment

ORF - retro_chof_1535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.62 %
• Parental protein coverage: 75.5 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FSEVTQPLMNVPIKGSGPHGPFPKKFYPRFTRGPSRVFEPQFKANKIGDMVDNQNDDPGKDSMKFSPELX
          FSEVTQPL.NVPIKGSGPHGP.PK.F...FT.G.S.V.EP.FKANK.GDM.DNQNDDPGKDSMKFSPEL.
Retrocopy FSEVTQPLKNVPIKGSGPHGPVPK*F*LHFTQGQSQVLEPLFKANKTGDMIDNQNDDPGKDSMKFSPELD

Parental  XXFNKHDQELRDLGYQKHAFNMLISNRLGYHRDVPDTRNALCKEKSYPTDLPIASIVVCFYNE-AFSALL
          ...N.H.QE.RDL.YQKHAFNMLI.NRLGYHR.V.DTRNA.CKEKSYPTDL..ASIV.CFY.E..FSAL.
Retrocopy MILNEHYQEMRDLSYQKHAFNMLI-NRLGYHRNVSDTRNAVCKEKSYPTDLLVASIV-CFYDE<SFSALF

Parental  RTVHSVIDRTPAHLLHEIILVDDDSDFDDLKGELDEYIQKYLPGKTKVIRNMKREGLIRG-RMIGAAHAT
          ..VHSVID.T.AHLLHEIILVD.DSDFD.LKGELDEYIQ..LPGKTKVIRN.K.EGLI...RMIGAA.AT
Retrocopy WIVHSVIDQTLAHLLHEIILVDNDSDFDYLKGELDEYIQNCLPGKTKVIRNTKHEGLIQK<RMIGAARAT

Parental  GEVLVFLDSHCEVNEMWLQPLLAVIQEDRKTVVCPVIDII-SADTLTYSSSPIVRGGFNWGLHFKWDLVP
          .EVLVFLD.HC.VNE..L.PLLA.I.ED..TVVC.VIDII..ADTL.YSSS.IV..GF.W.LHFKWDLVP
Retrocopy KEVLVFLDNHC*VNEV*L*PLLAAIHEDH*TVVCVVIDII<RADTLSYSSSSIV*EGFKWRLHFKWDLVP

Parental  LPELEGPEGATAPIKS-LMAGGLFAMNRQYFNELGQYDSGMDIWGGENLEISFRIWMCGGKLFIIPCSRV
          L.ELEGPE.ATAPIKS...AGGLFAMNRQYFNELGQYDSGMDIWGGENLEISF.IWM..GKLFI.P.SRV
Retrocopy LSELEGPEEATAPIKSPTVAGGLFAMNRQYFNELGQYDSGMDIWGGENLEISFWIWMYEGKLFI-PSSRV

Parental  GHIFRKRRPYGSPEGQDTMTHNSLRLAHVWLDEYKEQYFSLRPDLKTKNYGNISERVELRKKLGCKSFKW
          GHIF.KR.PYG.PEGQDTMTHNSLRLAHVWLDEYKEQYFSLRP.LKTK.YGNISE.V.LRKKLGCKSFKW
Retrocopy GHIFQKR*PYGFPEGQDTMTHNSLRLAHVWLDEYKEQYFSLRPALKTKSYGNISECVDLRKKLGCKSFKW

Parental  YLDNIYPQMQISGPNAQPQQPIFINRGPKRPKVL
          YLDNIYPQ.QISGPNA.PQQ.IFINR.PK.PK.L
Retrocopy YLDNIYPQIQISGPNAEPQQCIFINRRPKCPKIL

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_1535 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001121	1 retrocopy	retro_chof_1535 ,
Homo sapiens	ENSG00000178234	1 retrocopy	retro_hsap_402,
Gorilla gorilla	ENSGGOG00000008784	1 retrocopy	retro_ggor_399,
Nomascus leucogenys	ENSNLEG00000004613	1 retrocopy	retro_nleu_1573,
Pan troglodytes	ENSPTRG00000019891	1 retrocopy	retro_ptro_308,