RetrogeneDB ID: retro_chof_1910

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_420829:56..812(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDCBP
• Ensembl ID: ENSCHOG00000003565
• Aliases: None
• Description: syndecan binding protein (syntenin) [Source:HGNC Symbol;Acc:10662]

Sequence

>retro_chof_1910
CTCCATCCTAAACTGTATCCGGAGCTCTCTAAATATATGGGCCTGAGTCTAAATGAAGAAGAAATACATCCATATATGGC
CACGGTCCCTGGAGAACCAGTGCAGGGGTTGGTTGTAAGGCCTTCCAGTGTAAACTATATGGCGGCTTCTGTAACTGGTA
ATGATATTGGAATTCAAAGAGCAGAAATTAAGCAAGGAATTCATGAAGTTATTTTATGTAAGGATGAAAATGGAAAAATT
CGCCTCAGGCTTAAATCAGTAGATGATGGCTTATTTATCCAGATAGTCCAAGCTAATTCTCTAGCATCTTTGGTTGGTCT
GAAATTTGGGGATCAAGTACTTCAGATTAATAGTGAAAACTGTGCTGGCTGGAGCTCTGATGAAGCACACAAAGTGCTCA
AACAGGCTTTTGGAGAAAAGATTACTGTGACTATTCATGACAGCTCCTTTGAACGGACTATTATCATGCATAAAGATAGT
ACTGGACATGTTGGCTTTACCTTCAAAAATGGAAAAATAAAATCCATAGTGAAAGACAGCTCTGCAGCTGTTAATGGTCT
TCTCACAGAACACATCTGTGAAATCAATGGACAGAATGTCATTTGTTTGAAGAACTCTAAAATTGCAGACATACCTTTGA
CATCTGTGACTGTAGTTACTATTACTATCATGCCTGCTTTTATCTTTGAACATATTATGAAACAGATGGCACCAAGAATT
ATGAAAAGCTTGAAGGATCACAACATTCCTGAAGTT

Alignment

ORF - retro_chof_1910 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYPKLYPELSQYMGLSLNEDEVRANMVMVFGEPVQGQLVVRPSSVNYMVAPVTGNDVGIRRAEIKQGIRE
          L.PKLYPELS.YMGLSLNE.E....M..V.GEPVQG.LVVRPSSVNYM.A.VTGND.GI.RAEIKQGI.E
Retrocopy LHPKLYPELSKYMGLSLNEEEIHPYMATVPGEPVQG-LVVRPSSVNYMAASVTGNDIGIQRAEIKQGIHE

Parental  VILCKDQDGKIGLRLKSVDNGVFIQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGE
          VILCKD..GKI.LRLKSVD.G.FIQ.VQANS.ASLVGL.FGDQVLQIN.ENCAGWSSD.AHKVLKQAFGE
Retrocopy VILCKDENGKIRLRLKSVDDGLFIQIVQANSLASLVGLKFGDQVLQINSENCAGWSSDEAHKVLKQAFGE

Parental  KITMTIRDRPFERTITMHKDSSGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQT
          KIT.TI.D..FERTI.MHKDS.GHVGF.FKNGKI.SIVKDSSAA.NGLLTEH.ICEINGQNVI.LK.S..
Retrocopy KITVTIHDSSFERTIIMHKDSTGHVGFTFKNGKIKSIVKDSSAAVNGLLTEH-ICEINGQNVICLKNSKI

Parental  ADILSTSGTVVTITIMPAFIFEHIIKRMAPSIMKSLMDHTIPEV
          ADI..TS.TVVTITIMPAFIFEHI.K.MAP.IMKSL.DH.IPEV
Retrocopy ADIPLTSVTVVTITIMPAFIFEHIMKQMAPRIMKSLKDHNIPEV

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_1910 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 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006161	1 retrocopy	retro_amel_654,
Bos taurus	ENSBTAG00000019910	2 retrocopies	retro_btau_1035, retro_btau_383,
Canis familiaris	ENSCAFG00000007112	1 retrocopy	retro_cfam_112,
Choloepus hoffmanni	ENSCHOG00000003565	5 retrocopies	retro_chof_1063, retro_chof_1151, retro_chof_1910 , retro_chof_713, retro_chof_970,
Equus caballus	ENSECAG00000015053	1 retrocopy	retro_ecab_439,
Homo sapiens	ENSG00000137575	2 retrocopies	retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla	ENSGGOG00000009019	2 retrocopies	retro_ggor_2666, retro_ggor_2995,
Loxodonta africana	ENSLAFG00000010757	1 retrocopy	retro_lafr_1044,
Microcebus murinus	ENSMICG00000003968	1 retrocopy	retro_mmur_170,
Myotis lucifugus	ENSMLUG00000004807	1 retrocopy	retro_mluc_12,
Macaca mulatta	ENSMMUG00000017296	1 retrocopy	retro_mmul_2564,
Mustela putorius furo	ENSMPUG00000010339	5 retrocopies	retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys	ENSNLEG00000001408	2 retrocopies	retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii	ENSOGAG00000013462	1 retrocopy	retro_ogar_3259,
Procavia capensis	ENSPCAG00000016432	1 retrocopy	retro_pcap_186,
Pongo abelii	ENSPPYG00000018612	3 retrocopies	retro_pabe_3265, retro_pabe_3266, retro_pabe_3738,
Pan troglodytes	ENSPTRG00000020277	2 retrocopies	retro_ptro_2696, retro_ptro_3200,
Tupaia belangeri	ENSTBEG00000013965	1 retrocopy	retro_tbel_2142,