RetrogeneDB ID: retro_chof_2552

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_85275:9425..10013(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSCHOG00000012339
• Aliases: None
• Description: mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]

Sequence

>retro_chof_2552
CCTCAGCTGAACGCACAGCCAAAAGGTTGGCTTTCACACTCTGCGAAAAGACCTGCTAGAGCCATTACTGCACCCCACGC
AGGATATACGTACTGTGGATCTTGTGCTGCCCATGCTTACAAGCAAGTGGATCCATGTATTACCCAGAGAATTTTCATCC
CTGGGCCTTCCCATCATGTGCCCTTCTCTCGATGTGCACTTTTCAATGGGGATATACATAGGACACCTTCGCATGACTTT
CCTATTTTCCAAAAGATTTACGGAGAACTATGGGAGACAGGAATGTTTGAACGCATGTCTCTGCAGACAGATGAAGATGA
ACACGGTATTGAAAAGCATTTGCCTTACACAGCTAAAGCCATGGAAAGCCATAAGGATGAGTTTACCATTATTTCTGTAC
TGTTTGGAGCTCTGAGTGAATCAAAAGAATAGAAACTTGGAAAACTCTTCAATAAATATCTAGCAGATCCTAGTAATCTC
TTTGTGGTTTCTTCTGATTTCTGCTATTGGGGTCAAAAGTTCCATTACAATTACTGTGATGATTCCCAGGGGGAGATTTA
TAGATCCATTGAACATCTAGATAAAATG

Alignment

ORF - retro_chof_2552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQLNAQLEGWLSQVQSTKRPARAIIA-HAGYTYCGSCAAHAYKQVDPSITRRIFILGPSHHVPLSRCALS
          PQLNAQ..GWLS...S.KRPARAI.A.HAGYTYCGSCAAHAYKQVDP.IT.RIFI.GPSHHVP.SRCAL.
Retrocopy PQLNAQPKGWLSH--SAKRPARAITAPHAGYTYCGSCAAHAYKQVDPCITQRIFIPGPSHHVPFSRCALF

Parental  SVDIYRTPLYDLRIDQKIYGELWKTGMFERMSLQTDEDEHSIEMHLPYTAKAMESHKDEFTIIPVLVGAL
          ..DI.RTP..D..I.QKIYGELW.TGMFERMSLQTDEDEH.IE.HLPYTAKAMESHKDEFTII.VL.GAL
Retrocopy NGDIHRTPSHDFPIFQKIYGELWETGMFERMSLQTDEDEHGIEKHLPYTAKAMESHKDEFTIISVLFGAL

Parental  SESKEQEFGKLFSKYLADPSNLFVVSSDFCHWGQRFRYSYYDES-GEIYRSIEHLDKM
          SESKE...GKLF.KYLADPSNLFVVSSDFC.WGQ.F.Y.Y.D.S.GEIYRSIEHLDKM
Retrocopy SESKE*KLGKLFNKYLADPSNLFVVSSDFCYWGQKFHYNYCDDSQGEIYRSIEHLDKM

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_2552 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012339	2 retrocopies	retro_chof_2257, retro_chof_2552 ,
Cavia porcellus	ENSCPOG00000012278	1 retrocopy	retro_cpor_1159,
Dasypus novemcinctus	ENSDNOG00000001254	1 retrocopy	retro_dnov_253,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Pteropus vampyrus	ENSPVAG00000011427	1 retrocopy	retro_pvam_184,