RetrogeneDB ID: retro_chof_2013

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_45466:9822..10689(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TWF1
• Ensembl ID: ENSCHOG00000008386
• Aliases: None
• Description: twinfilin actin-binding protein 1 [Source:HGNC Symbol;Acc:9620]

Sequence

>retro_chof_2013
TTCCTGGAGCTGCCAGCCAGGGCTGCTTGCTGCACTTGGTACTGGATCTTGGAGCCAGTGGCTGCTGCCATGTCCCACCA
GACTGTCATGAAAGCTAGTGAAGATATTAAAGACATCCTTGCCAGAGCAAGAAATGGAAAATACAGACTTCTGAAAATAT
TTATTGAAAATGAGCAATTTGTGATTTGGTCGTGTAGTCAACCTTTAGATTCCTGGGATAAAGATTATGATTTCTTTGTT
CTACCCTGTTGGAGGACAAACAACCATGCTATATATTATTCAGAGTAGATTCCAAGAATGCTCAGGGATATGAATGGATA
TTCATTCCATGGTCTTCATATCATTCTCATGTTCATTGGAAAATGTACATGGCAACAAGAGCAGTTCTAAAGAAGGAGTT
TGGAGGTGGCCACATTAAAGATGAAGTATTTGGAACAGTAAAGAAAGATGTATCATTACCTGCATATAAAAATATTTGCT
ATCATGATCTTCCCCTGCCCTGTTAATGCAGCTGAAGAAGAATTATGACAGATTAAAATTAATGAGGTACAAACTGATGT
GAGGGAGGACACTGTGCATCAAACACTAAAAGGGGTAGCATTTCCTATTTCTCAGGAAGATTTTCAGCCTTTGGAAAAAT
TGAATAACAGACAGCTCAACTATGTGCAGTTGGAAATAGATATAAAAAATGAAATTATAATTTTGGTGAACACAGCAACT
ACAGAACAAAAAGATTTGCCAAACAGGATTCCCAAAGATTCAGCACATTACCATTTCTTTCTGTATAAATGTTCCCATGA
AGGAGACTATTTGGAGTCCATAGTTTTTCTTTATTCAATGCCTGGATATACATGCAGTATAAGAGAA

Alignment

ORF - retro_chof_2013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.29 %
• Parental protein coverage: 75.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FLEPPAGAAGCSQWRIPEPAAAAMSHQTGIQASEDVKDIFARARNGKYRLLKISIENEQLVIGSCSQPSD
          FLE.PA.AA.C....I.EP.AAAMSHQT...ASED.KDI.ARARNGKYRLLKI.IENEQ.VI.SCSQP.D
Retrocopy FLELPARAACCTWYWILEPVAAAMSHQTVMKASEDIKDILARARNGKYRLLKIFIENEQFVIWSCSQPLD

Parental  SWDKDYDSFVLP-LLEDKQPCYILFRLDSQNAQGYEWIFIAWSPDHSHVRQKMLYAATRATLKKEFGGGH
          SWDKDYD.FVLP.LLEDKQPCYILFR.DS.NAQGYEWIFI.WS..HSHV..KM.Y.ATRA.LKKEFGGGH
Retrocopy SWDKDYDFFVLP<LLEDKQPCYILFRVDSKNAQGYEWIFIPWSSYHSHVHWKM-YMATRAVLKKEFGGGH

Parental  IKDEVFGTVKEDVSLHGYK-KYLLSQSSPA-PLTAAEEELRQIKINEVQTDVSVDTKHQTLQGVAFPISQ
          IKDEVFGTVK.DVSL..YK.KYLLS.SSPA.P..AAEEEL.QIKINEVQTDV..DT.HQTL.GVAFPISQ
Retrocopy IKDEVFGTVKKDVSLPAYK<KYLLS*SSPA<PVNAAEEEL*QIKINEVQTDVREDTVHQTLKGVAFPISQ

Parental  EAFQALEKLNNRQLNYVQLEIDIKNEIIILANTTNTELKDLPKRIPRDSARYHFFLYKHSHEGDYLESIV
          E.FQ.LEKLNNRQLNYVQLEIDIKNEIIIL.NT..TE.KDLP.RIP.DSA.YHFFLYK.SHEGDYLESIV
Retrocopy EDFQPLEKLNNRQLNYVQLEIDIKNEIIILVNTATTEQKDLPNRIPKDSAHYHFFLYKCSHEGDYLESIV

Parental  FIYSMPGYTCSIKE
          F.YSMPGYTCSI.E
Retrocopy FLYSMPGYTCSIRE

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_2013 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017332	1 retrocopy	retro_amel_1224,
Choloepus hoffmanni	ENSCHOG00000008386	5 retrocopies	retro_chof_1525, retro_chof_2013 , retro_chof_2569, retro_chof_391, retro_chof_509,
Homo sapiens	ENSG00000151239	2 retrocopies	retro_hsap_1819, retro_hsap_4916,
Monodelphis domestica	ENSMODG00000018535	1 retrocopy	retro_mdom_167,
Mustela putorius furo	ENSMPUG00000000364	1 retrocopy	retro_mputfur_1629,
Mus musculus	ENSMUSG00000022451	1 retrocopy	retro_mmus_2961,
Nomascus leucogenys	ENSNLEG00000017931	1 retrocopy	retro_nleu_2877,
Otolemur garnettii	ENSOGAG00000007525	1 retrocopy	retro_ogar_1058,
Pan troglodytes	ENSPTRG00000004846	1 retrocopy	retro_ptro_3279,
Rattus norvegicus	ENSRNOG00000022507	1 retrocopy	retro_rnor_2176,