RetrogeneDB ID: retro_chof_1525

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_315757:192..1306(+)
• 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_1525
CACTTCCTGGAGCTGTGGGCCAGGGCCACTCACTGCAGTCAGTGGCAGATCCCGGAGCCTGCGGCTGCTGCCATGTCCCA
TCAGACCAGCATCCAAGCTAGTGAAGATGTTAAAGATATCTTTGCCAGAGCAAGAAATGGAAAATACAGACTTCTGAAAC
TACCTATTGAAAATGAGCAAATTGTGATTGGGTCATGTAGTCAACCTTCAGATTCCTGGGATAAGGATTATGATTCCTTT
GTTCTACCCCTCCTGGAGGACAAATAACCATGCTATATATTATTCAGATTAGATTCCCAGAATGCCCAGGCATATGAATG
GATATTCATTGCATGGTCTCCAGATCATTCTCACGTTCATCAGAAAATGTATGCAGCAACAAGAGCAACTCTAAAGAAGG
AGTTTGGAGGTGGCCACATTAAAGATGAAGTATTTGGAACAGTAAAGGAAGATGTATCATTACATGGATATAAAAAATAT
TTGTTATCACAATCTTCCCCTGCCCCACTGGCTGCAGCAGAGGAAGAATTATGACAAATTAAAATTAATGAGGTACAAAC
TGATGTGAGTGTAGACACTAAGCATCAAACACTACAAGGGGTAGCATTTCCTATTTTGCAGGAAGCTTTTCAGGCTTTGG
AAAAATTGAATAACAGCTCAACTACATGCAGTTGGAAATAGATATAAAAAATGAAATTATAATTTTGGCCAACACAACAA
ATACAGAACTAAAAGATTTGCCAAAGAGGATTTCCAGAGATTCAGCACATTATCACTTCTTTCTGTATAAACATTCCCAT
GAAGGAGACTATTTGGAGTCCATAGTTCTTATTTATTCAATGACTGGATACACATGCAATATAAGAGAATGGATGCTGTA
TTCTAGCTGCAAGAGCCCTCTGCTAGAAATTGTAGAAAGACAACTACAAATGGATGTATTAGAAAGACTGAGATAGATAA
TGGGGATGAATTGACTGCAGAATTCCTTTATGAAGAAGTACACCCTGAGCAACATTCTCATAAGCAAAGTTTTGCAAAAC
CAAAAGGTCCTGCAGGAAAAAGAGGATTTCAAAGACTAATTTGCAGTCCAGCTGAAACTGAAGTCACTACTGAT

Alignment

ORF - retro_chof_1525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.24 %
• Parental protein coverage: 97.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HFLEPPAGAAGCSQWRIPEPAAAAMSHQTGIQASEDVKDIFARARNGKYRLLKISIENEQLVIGSCSQPS
          HFLE..A.A..CSQW.IPEPAAAAMSHQT.IQASEDVKDIFARARNGKYRLLK..IENEQ.VIGSCSQPS
Retrocopy HFLELWARATHCSQWQIPEPAAAAMSHQTSIQASEDVKDIFARARNGKYRLLKLPIENEQIVIGSCSQPS

Parental  DSWDKDYDSFVLPLLEDKQPCYILFRLDSQNAQGYEWIFIAWSPDHSHVRQKMLYAATRATLKKEFGGGH
          DSWDKDYDSFVLPLLEDK.PCYILFRLDSQNAQ.YEWIFIAWSPDHSHV.QKM.YAATRATLKKEFGGGH
Retrocopy DSWDKDYDSFVLPLLEDK*PCYILFRLDSQNAQAYEWIFIAWSPDHSHVHQKM-YAATRATLKKEFGGGH

Parental  IKDEVFGTVKEDVSLHGYKKYLLSQSSPAPLTAAEEELRQIKINEVQTDVSVDTKHQTLQGVAFPISQE-
          IKDEVFGTVKEDVSLHGYKKYLLSQSSPAPL.AAEEEL.QIKINEVQTDVSVDTKHQTLQGVAFPI.QE.
Retrocopy IKDEVFGTVKEDVSLHGYKKYLLSQSSPAPLAAAEEEL*QIKINEVQTDVSVDTKHQTLQGVAFPILQE<

Parental  AFQALEKLNNRQLNYVQLEIDIKNEIIILANTTNTELKDLPKRIPRDSARYHFFLYKHSHEGDYLESIVF
          .F....K....QLNY.QLEIDIKNEIIILANTTNTELKDLPKRI.RDSA.YHFFLYKHSHEGDYLESIV.
Retrocopy SFSGFGKIE*-QLNYMQLEIDIKNEIIILANTTNTELKDLPKRISRDSAHYHFFLYKHSHEGDYLESIVL

Parental  IYSMPGYTCSIKERMLYSSCKSPLLEIVERQLQMDV-IRKXXXXXXXXXXXXXXFEEAYPKQHAQKPSFA
          IYSM.GYTC.I.E.MLYSSCKSPLLEIVERQLQMDV.IRK...............EE..P.QH..K.SFA
Retrocopy IYSMTGYTCNIREWMLYSSCKSPLLEIVERQLQMDV<IRKTEIDNGDELTAEFLYEEVHPEQHSHKQSFA

Parental  KPRGPAGKRGILRLIGGPAETEATTD
          KP.GPAGKRG..RLI..PAETE.TTD
Retrocopy KPKGPAGKRGFQRLICSPAETEVTTD

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_1525 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,