RetrogeneDB ID: retro_chof_278

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_6108:12409..13198(+)
• Located in intron of: ENSCHOG00000011884

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNTB1
• Ensembl ID: ENSCHOG00000007627
• Aliases: None
• Description: syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1) [Source:HGNC Symbol;Acc:11168]

Sequence

>retro_chof_278
ACCTTGATCCTGCGCTGCAAGGATACAGCCACAGCACACTCCTGGTTCGTAGCTATCCACACCAACATAATGGCTCTCCT
CCCACAGGTGTTGGCTGAACTCAATGCCATACTTGGTGCAACCAGTGCGGCAGGAGGCAGTAAGGAGGTCAGGCACATTG
CCTGGCTGGCAGAACAGGCAAAACTAGATGGTGGAAGACAACAATGGAGACCTGTCCTCATGGCTGTGACTGAGAAGGAT
TTGCTGCTTTATGACTGTATGCCATGGACAAGGGATGCTTGGGCATCACCATGTCATAGCTACCCTCTTGTTGCCACAAG
GTTGGTTCATTCTGGTTCCGGATGTCGATCACCTTCACTTGGATCTGATCTTACATTTGCTACCAGGACAGGCTCTCGGC
AGGGCATTGAAATGCATCGTTTCAGGGTGGAGACACATTGGGATCTGTCAACTTGGACCAGGATACTTGTTCAAGGTTGT
CACGCTGCTGCTGAGCTGATCAAGGAAGTCTCTCTAGGGTGCACATTAAATGGCCAAGAGGTAAGACTCACTGTTCACTA
TGAAAATGGATTCACTATCTCCAGGGAAAATGGAGGCTCCAGCAGCATATTGTACTGCTACCCCTTTGAAGGGCTGAAAA
TGTCTGCTGATGATGGCATCAGAAATCTGTATCTGGATTTTGGTGGTCGTGAGGGAGAACTGACCATGGACCTACACTCT
TGTCCAAAGCCGATTGTATTTGTGTTGCACACGTTCTTGTCAGCCAAAGTCACTCGCATGGGACTGCTT

Alignment

ORF - retro_chof_278 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.87 %
• Parental protein coverage: 75.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TVILRSKDSATAQAWFSAIHANVSDLLSRVIAEVREQLGKTDIAG-SREIRHLGWLAEKVPGES-EKQWK
          T.ILR.KD.ATA..WF.AIH.N...LL..V.AE....LG.T..AG.S.E.RH..WLAE.........QW.
Retrocopy TLILRCKDTATAHSWFVAIHTNIMALLPQVLAELNAILGATSAAGGSKEVRHIAWLAEQAKLDGGRQQWR

Parental  PALVVLTEKDLLIYDSMPRRKEAWLSPVHTYPLLATRLVHSGPGKGSPQAGMDLSFATRTGTRQGIETHI
          P.L...TEKDLL.YD.MP....AW.SP.H.YPL.ATRLVHSG.G..SP..G.DL.FATRTG.RQGIE.H.
Retrocopy PVLMAVTEKDLLLYDCMPWTRDAWASPCHSYPLVATRLVHSGSGCRSPSLGSDLTFATRTGSRQGIEMHR

Parental  FRAEISRDLSHWTRSIVQGCHNSAELITEITAACTYKNQECRLTIHYENGFSITTEPQEGAFPKTIIQSP
          FR.E...DLS.WTR..VQGCH..AELI.E....CT...QE.RLT.HYENGF.I..E...G.........P
Retrocopy FRVETHWDLSTWTRILVQGCHAAAELIKEVSLGCTLNGQEVRLTVHYENGFTISRE--NGGSSSILYCYP

Parental  YEKLKMSSDDGIRMLCLDFGGKDGEIQLDLHSCPKPIVFIIHSFLSAKITRLGLV
          .E.LKMS.DDGIR.L.LDFGG..GE...DLHSCPKPIVF..H.FLSAK.TR.GL.
Retrocopy FEGLKMSADDGIRNLYLDFGGREGELTMDLHSCPKPIVFVLHTFLSAKVTRMGLL

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_278 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	ENSCHOG00000007627	1 retrocopy	retro_chof_278 ,