RetrogeneDB ID: retro_chof_1155

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_21421:4656..5429(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL14EP
• Ensembl ID: ENSCHOG00000012698
• Aliases: None
• Description: ADP-ribosylation factor-like 14 effector protein [Source:HGNC Symbol;Acc:26798]

Sequence

>retro_chof_1155
ATGATGGATCCCTGTTCAGTTGGAGTCCAGCTTCGTACCACAAATGAGTGCCATAAAACATACCATACTCGTCATACAGG
TTTCAAGACTTTGCAAGAATTGTCATCAAATGATATGCTTTTACTTCAACTTAGAACTGGAATGACACTTTCTGGGAATA
ACACAATCTGCTTCCATCATGCAAAAATTTACATTGACCGATTTGAAGATTTGCAGAAGTCGTGTTGTGACCCATTTAAC
ACACACAAACTACTAGTCAAAAAAAATTTGCATGGAATTGATTTAGATGATGCCACTTTCCTGAGTGCAAAATTTGGAAG
GCAGCTTGTACCTGGGTGGAAGCTTTGTCCAAAATGTACACAGGTAATCAATGGAAGTGTGGATACTGATTCTGAAGACC
ATCAGAGAAGAAAACCTGATTCAGATGGAAGAACTGCTAAAGCTTTAAGGTCATTACAGTTTATAAACTCAGAAAGCAAA
CTGAATTTTCTCCAGAAACTGGTAAAAGAGAAAAAAGAAGGCTTACAAAAAATGCATCAGCTGGTTCAGACAGACAAGTG
ATACCAGCAAAGAGTAAGGTCTACGATAGTCAGGGTCTCCTGATTTTCAGTGGGATGGATCTCTGTGACTGCCTTGATGA
AGCCTGCTTAGGATGTTTCTATGCTTGTCCTGCTTGTGTTTCTACCAAATGTGGAGCTGAATGCCATTGTGACCACAAGT
AGCTGTATGAGAAAATTGAAATAGAAGGAGGAGAAATAATTCATAATAAACAT

Alignment

ORF - retro_chof_1155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.26 %
• Parental protein coverage: 99.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMDPCSVGVQLRTTNECHKTYYTRHTGFKTLQELSSNDMLLLQLRTGMTLSGNNTICFHHAKIYIDRFED
          MMDPCSVGVQLRTTNECHKTY.TRHTGFKTLQELSSNDMLLLQLRTGMTLSGNNTICFHHAKIYIDRFED
Retrocopy MMDPCSVGVQLRTTNECHKTYHTRHTGFKTLQELSSNDMLLLQLRTGMTLSGNNTICFHHAKIYIDRFED

Parental  LQKSCCDPFNIHKKLAKKNLHVIDLDDATFLSAKFGRQLVPGWKLCPKCTQIINGSVDIDSEDRQRRKPD
          LQKSCCDPFN.HK.L....LH.IDLDDATFLSAKFGRQLVPGWKLCPKCTQ.INGSVD.DSED.QRRKPD
Retrocopy LQKSCCDPFNTHKLLVXXXLHGIDLDDATFLSAKFGRQLVPGWKLCPKCTQVINGSVDTDSEDHQRRKPD

Parental  SDGRTAKALRSLQFTNP-GKQTEFAPETGKREKRRXXXXXXXXXXXQVIPAKSKVYDSQGLLIFSGMDLC
          SDGRTAKALRSLQF.N...KQTEF.PETGKREKRR...........QVIPAKSKVYDSQGLLIFSGMDLC
Retrocopy SDGRTAKALRSLQFINS<RKQTEFSPETGKREKRRLTKNASAGSDRQVIPAKSKVYDSQGLLIFSGMDLC

Parental  DCLDEDCLGCFYACPACGSTKCGAECRCDRKWLYEQIEIEGGEIIHNKH
          DCLDE.CLGCFYACPAC.STKCGAEC.CD.K.LYE.IEIEGGEIIHNKH
Retrocopy DCLDEACLGCFYACPACVSTKCGAECHCDHK*LYEKIEIEGGEIIHNKH

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_1155 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012417	1 retrocopy	retro_btau_1266,
Choloepus hoffmanni	ENSCHOG00000012698	1 retrocopy	retro_chof_1155 ,
Felis catus	ENSFCAG00000028620	1 retrocopy	retro_fcat_437,
Microcebus murinus	ENSMICG00000011547	2 retrocopies	retro_mmur_1003, retro_mmur_131,
Macaca mulatta	ENSMMUG00000017590	2 retrocopies	retro_mmul_1793, retro_mmul_984,
Mus musculus	ENSMUSG00000027122	1 retrocopy	retro_mmus_3319,