RetrogeneDB ID: retro_chof_2240

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_60344:3303..4144(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK14
• Ensembl ID: ENSCHOG00000012973
• Aliases: None
• Description: cyclin-dependent kinase 14 [Source:HGNC Symbol;Acc:8883]

Sequence

>retro_chof_2240
TCTCTGTTAAAAGGACTAAAACATGCTAACATAGTGCTGCTTCATGACATCATCCACACAAGGGAGATACTGACACTTGG
GTTTGAATATGTGCACACTGATTTATGTCAGTACATGGACAAGCACGCTGGGGGTGCTGCATCCAGACAATGTGAAGTTG
TTTTGATTTCAGTTGCTATGAGGGCTGCATTACATCTACAAGGGGTTTATTTTGCATAGAGACCTGAAGCCACAGAACCT
TCTGATCAGTGACATGGAGGAGTTAAAGCTGGCAGATTTTGGTCTTGCCAGAGCAAAATCCGTCCCTAGTCACACATACT
CCAAGGAAGTGGTTACCTTGTGGTATAGACCTCCAGATGTTTTCCTGGGCTCAATAGAATAGTCTACCTGCCTTAACATA
ACGGGAGTCGGTTGCATCTTTGTTGAAATGATTCAAGGGGTTGCTGCTTTTCTGGGAATGAAAGACATTCAGGATCAACT
TGAACAAGTGTTTCTGTTCCTTGGAACACCAAGTAACACATGACCTGGAGTTCATTCTTTACCACATTTTAAGCCAGAAT
GCTTTACGCTGTACAGCTCTAAAATCCTTAGACAAGCTTGGAATAAGCTTATCTATGTCAATCATGCAGAAGATCTGGCT
TCCAAGCTCGTACAATGTTCCCCAAAGAACAGACTATCAGCACAGGCACCAATGAGCCATGAGTATTTCAGTGACCTGCC
TCTGCAGCTATGGGAACTGACTGACTTATCTTCTATTTTTACCGTCCCAAATGTATGATTGCAACCAGAAGCTGGAGAAA
GCATGCAGGCCTTTGGGAAAAACAACAGTTATGGCAAAAGT

Alignment

ORF - retro_chof_2240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.79 %
• Parental protein coverage: 59.83 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLLKGLKHANIVLLHDIIHTKETLTLVFEYVHTDLCQYMDKHPGG-LHPDNVKLFLFQLLRGLSYIHQRY
          SLLKGLKHANIVLLHDIIHT.E.LTL.FEYVHTDLCQYMDKH.GG.LHPDNVKLF.FQLL.GL.YI....
Retrocopy SLLKGLKHANIVLLHDIIHTREILTLGFEYVHTDLCQYMDKHAGG>LHPDNVKLF*FQLL*GLHYIYKGF

Parental  ILHRDLKPQNLLISDTGELKLADFGLARAKSIPSHTYSNEVVTLWYRPPDVLLGSTEYSTCLDMWGVGCI
          ILHRDLKPQNLLISD..ELKLADFGLARAKS.PSHTYS.EVVTLWYRPPDV.LGS.E.STCL...GVGCI
Retrocopy ILHRDLKPQNLLISDMEELKLADFGLARAKSVPSHTYSKEVVTLWYRPPDVFLGSIE*STCLNITGVGCI

Parental  FVEMIQGVAAFPGMKDIQDXXXXXXXVLGTPNEDTWPGVHSLPHFKPERFTLYSSKNLRQAWNKLSYVNH
          FVEMIQGVAAF.GMKDIQD........LGTP...T.PGVHSLPHFKPE.FTLYSSK.LRQAWNKL.YVNH
Retrocopy FVEMIQGVAAFLGMKDIQDQLEQVFLFLGTPS-NT*PGVHSLPHFKPECFTLYSSKILRQAWNKLIYVNH

Parental  AEELASKLLQCSPKNRLSAQAALSHQYFSDLPPRLWELTDXXXXXXXXNVRWQPEAGESMRA-GKNNSYG
          AE.LASKL.QCSPKNRLSAQA..SH.YFSDLP..LWELTD........NV..QPEAGESM.A.GKNNSYG
Retrocopy AEDLASKLVQCSPKNRLSAQAPMSHEYFSDLPLQLWELTDLSSIFTVPNV*LQPEAGESMQAFGKNNSYG

Parental  KS
          KS
Retrocopy KS

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_2240 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012973	1 retrocopy	retro_chof_2240 ,
Choloepus hoffmanni	ENSCHOG00000013679	1 retrocopy	retro_chof_46,
Callithrix jacchus	ENSCJAG00000014175	1 retrocopy	retro_cjac_4070,