RetrogeneDB ID: retro_chof_1345

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_26867:12140..13061(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007548
• Aliases: None
• Description: None

Sequence

>retro_chof_1345
TTTATAAGCACAATGGCACCGATGGAGGGCAATGCACCAGAGACTATATACAGCATGAATGAGGAAGGTTGGAGGAGAGC
AGTGTAGCAGAATACTATGAAATGATTGAACTGAACAAACTGGAACACAGCCTCTGGCAACATCCTTTCACAATAGAATG
AATGCCTTTGTGGACATGACCAATGAAGAATTCAGAGAGGTGATGAATGGATTTCAAAACCAGGAACACAAGAAGGGGAA
AATGTTCTATGAGCCTCCCTCTGAGGTCCCCAAATCTGTGGACTGGCGTAACAAAGGCTACATGACTCCTTTGAAGGATC
AGGTTCAGTGAGGTTCTTGATGGGCTTTCAGTGCAACCAGTTCCCATGAAGGACAGATGTTCCAGAAAACTGGAAAACTG
GTTTCACTCAGTGAGCAGAACCTGGTGGACAGCACTCAGGCTGAGGGCAATAAAGGCTGCAATGGTGGCCTAATGGACAA
TGCTTCCCAGTATGTCCAGGATAACAGAAGCCTCAATTTAGAGAAATCCTATCCATGTATTGGAAAGGACATGACTTGAT
GCTACAAGACCAAATATTTTGCTGCCAATGACACTGGCTTCATGGACATTCCCCCACGGTTGAAAGCACCTATGAAGGCA
GTGGCAACTGTAGGACCCAGTTCTGTTGCTATCGATGTAAGCCATGACTGCTTCCAGTTCTGCTCATCAGCACTTATTTT
GAGCTGGGCTGCAGCAGCAAAGACCTGGATCATGGTGTTCTGCTGGTCAACTATGGCTTTGGAGGAGCAGATTTAGATTA
CAGTAAATACTGTTGCATCAAGGACAGCTGGAGTGAAAACTGGGGCATGGAGGGCGATGTAAAGATGGCCAGAGAGTGGA
ACAACCACTGTGGAGTTGCCGCATCAGCCAGCTATCCCACC

Alignment

ORF - retro_chof_1345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.38 %
• Parental protein coverage: 98.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FLTALCLEIASAVPKFDSSSEEDWRRAVWEKNMK-IIEVHNQEYSLGQHSFKLG-MNAFGDMTSEEFRQV
          F..........A.....S..EE.WRRAV....MK..IE....E.SL.QH.F....MNAF.DMT.EEFR.V
Retrocopy FISTMAPMEGNAPETIYSMNEEGWRRAV*QNTMK<MIELNKLEHSLWQHPFTIE<MNAFVDMTNEEFREV

Parental  MNGFQNKEHKKGEMFSESPSEVPTSVDWRDKGYVTPVKNQGHCGSCWAFSAAGSLEGQMFRKTGILVSLS
          MNGFQN.EHKKG.MF.E.PSEVP.SVDWR.KGY.TP.K.Q...GS.WAFSA..S.EGQMF.KTG.LVSLS
Retrocopy MNGFQNQEHKKGKMFYEPPSEVPKSVDWRNKGYMTPLKDQVQ*GS*WAFSATSSHEGQMFQKTGKLVSLS

Parental  EQNLVDCSRAEGNSGCNGGLMDNAFQYVQDNKGLDSEESYPYVGKDMNCSYKPEYSAANDTGFVEVAPLE
          EQNLVD...AEGN.GCNGGLMDNA.QYVQDN..L..E.SYP..GKDM...YK..Y.AANDTGF....P..
Retrocopy EQNLVDSTQAEGNKGCNGGLMDNASQYVQDNRSLNLEKSYPCIGKDMT*CYKTKYFAANDTGFMDIPPRL

Parental  KTLMAAVAAVGPISVAIDASHESFQFYESGI-YYEPDCSSKDLDHGVLVVGYGFEETDSDNNKYWLVKNS
          K..M.AVA.VGP.SVAID.SH..FQF..S...Y.E..CSSKDLDHGVL.V.YGF...D.D..KY...K.S
Retrocopy KAPMKAVATVGPSSVAIDVSHDCFQFCSSAL<YFELGCSSKDLDHGVLLVNYGFGGADLDYSKYCCIKDS

Parental  WGESWGMEGYVKMARDRDNHCGIATKASYPT
          W.E.WGMEG.VKMAR...NHCG.A..ASYPT
Retrocopy WSENWGMEGDVKMAREWNNHCGVAASASYPT

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_1345 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007548	8 retrocopies	retro_chof_1227, retro_chof_1332, retro_chof_1345 , retro_chof_141, retro_chof_1464, retro_chof_2392, retro_chof_383, retro_chof_424,
Dasypus novemcinctus	ENSDNOG00000012037	1 retrocopy	retro_dnov_2387,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Otolemur garnettii	ENSOGAG00000001349	2 retrocopies	retro_ogar_1053, retro_ogar_1373,
Ochotona princeps	ENSOPRG00000001030	2 retrocopies	retro_opri_186, retro_opri_499,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Tupaia belangeri	ENSTBEG00000016406	1 retrocopy	retro_tbel_2841,