RetrogeneDB ID: retro_chof_1682

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_358082:376..915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN3
• Ensembl ID: ENSCHOG00000003785
• Aliases: None
• Description: tetraspanin 3 [Source:HGNC Symbol;Acc:17752]

Sequence

>retro_chof_1682
GGCCAGTTTGGTGTCACCTCCTCTAAGACCATGCTGGTCTTTCTCAACCTTGTCTTCTAGGGGACAGCTGACATTTTATG
CTGTATGGGAGCCAGTGTCTTCATCACTTATGACGAGCATGACCACTTCTTTGGAAATGTGTACCCTCTCATCCCTGCTG
TAGTGGTCATGGCGTAGGAGCCCAGCTTTTCATGATTGGGCTAATTGGCTGCTGAGTCACAATCCGGGAATACCACTGCG
GACTTGCCACATTTTTCATCCTCCTCAACTTGGTTTTTGTCATAGAAGTTGTAGTGATTTGGGGATACATTTACAGAGCA
AAGGTGGCAAATGGGGTTGATCACAGCATTTAGAAAGTATGTAAGATCTACAATGGTACCAGCTCTGAGGCTGCCAGTTG
AGCTATTGATTATGTACAGAGACAGCTGTCCTGTAGTAGAATTCACAGCTACTCAGACTGGGAAAACACAGACTGGTTTG
AAGAAACCAAAAACCAGAGTGTCCCTCTTAGCTGTTTAAGAGAGATTGCCAGCAGCTGT

Alignment

ORF - retro_chof_1682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.18 %
• Parental protein coverage: 71.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GQCGITSSKTVLVFLNLIFWGAAGILCYVGAYVFITYDDYDHFFEDVYTLIPAVVIIA-VGALLFIIGLI
          GQ.G.TSSKT.LVFLNL.F.G.A.ILC..GA.VFITYD..DHFF..VY.LIPAVV..A.VGA.LF.IGLI
Retrocopy GQFGVTSSKTMLVFLNLVF*GTADILCCMGASVFITYDEHDHFFGNVYPLIPAVVVMA<VGAQLFMIGLI

Parental  GCCATIRESHCGLATFVIILLLVFVTEVVVVVLGYVYRAKVENEVDRSIQKVYKTYNGTSPDAASRAIDY
          GC..TIRE.HCGLATF.I.L.LVFV.EVVV...GY.YRAKV.N.VD.SI.KV.K.YNGTS..AAS.AIDY
Retrocopy GC*VTIREYHCGLATFFILLNLVFVIEVVVI-WGYIYRAKVANGVDHSI*KVCKIYNGTSSEAAS*AIDY

Parental  VQRQLHCCGIHNYSDWENTDWFKETKNQSVPLSCCRETASSC
          VQRQL.C..IH.YSDWENTDWF.ETKNQSVPLSC.RE.ASSC
Retrocopy VQRQLSCSRIHSYSDWENTDWFEETKNQSVPLSCLREIASSC

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_1682 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009727	1 retrocopy	retro_amel_1275,
Bos taurus	ENSBTAG00000002415	2 retrocopies	retro_btau_1089, retro_btau_1650,
Canis familiaris	ENSCAFG00000018068	2 retrocopies	retro_cfam_1391, retro_cfam_571,
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682 ,
Choloepus hoffmanni	ENSCHOG00000010760	2 retrocopies	retro_chof_116, retro_chof_307,
Dasypus novemcinctus	ENSDNOG00000005619	3 retrocopies	retro_dnov_1371, retro_dnov_1520, retro_dnov_1616,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872,
Felis catus	ENSFCAG00000025746	1 retrocopy	retro_fcat_1860,
Mustela putorius furo	ENSMPUG00000017332	2 retrocopies	retro_mputfur_1641, retro_mputfur_1651,
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394,
Ictidomys tridecemlineatus	ENSSTOG00000005615	1 retrocopy	retro_itri_1268,