RetrogeneDB ID: retro_chof_1478

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_303125:40..1143(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX5
• Ensembl ID: ENSCHOG00000010128
• Aliases: None
• Description: sorting nexin 5 [Source:HGNC Symbol;Acc:14969]

Sequence

>retro_chof_1478
CTTAAAGCAATAAATGTAGATCTTCAAAGTGATGCTGCTCTGCAGGTGGACATTTCTGATGCTCTTAGTGAGAGGGATAA
AGTAAAATTCACTGTTCACACAAAGAGTTCATTGCCAAATTTTAAACAAAATGAATTTTCTGTTGTTTGACAACATGAGG
AATTCATTTGGCTTAACGATTCCTTCATTGAAAATGAAGACTATGTAGGTTACATTATCCCACCAGCACCACCAAGACCT
GATTTTGATGCTTCAAGGGAAAAACTACAGAAGCTTGGAGAAGGAGAAGGGTTAGTGACGAAGGAAGAATTCACAAAGAT
GAAACAGGAACTGGAAGCTGAATATTTGGCAATATTCAAGAAGACAGTTGCAATGCATGAAGTATTCCTGTGCTGTGTGG
CAGCACACCCAATTTGAGAAAAGATTTAAATTTGCATGTCTTCTTGGAATATAATCAAGATTGGAGTGTGTGAGGAAAAA
AGAAAAAAGAAAAACTTGAAGATTTCTTTAAAAACATGGTTAAATCAGCAGATGGAGTAATTGTTTCAGGAGTAAAGGAT
GTAGATGATTTCTTTGAGCATGAATGAACATTTCTTTTAGAATATCATAACTGAGTTAAGGATGCATCTGCTAAATCTGA
TAGGATGACACGATCACACAAAAGTGCTGCAGATGATTACAATAGGATTGGTTCTTCATTATACGCTTTAGGAACTCAGG
ATTCTACAGATATATGCAAATTTTTTCTCAAAGTTTCAGAACTGTTTGATAAAACCAGGCAAATAGAAGCACGAGTATCT
GTTGATGAAGACCTCAAACTTTCTGACCTTTTAAAATATTACTTAAGAGAATCTCAAGCTTCTAAGGAACTCCTTTATAG
AAGATCTAGGTTACTAGTGGATTATGAAAATGCTAATAAAGCACTTGATGAAGCAAGAGCAAAAAATAAAGATGTTCTGC
AGGCTGAAACTTCCCAACAATTATGTTGTCAGAAATTTGAAAAAATATCTGAATCTGCAAAACAAGAACTCATAGATTTC
AAGACAAGAAGAGTTGCTGCATTCAGAAAAAATTTAGTGGAACTCACAGAGTTAGAACTAAAA

Alignment

ORF - retro_chof_1478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.35 %
• Parental protein coverage: 95.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRSVSVDLNIDPSLQIDIPDALSERDKVKFTVHTKTTLSTFQSPEFSVTRQHKDFVWLHDTLNETTDYAG
          L....VDL..D..LQ.DI.DALSERDKVKFTVHTK..L..F...EFSV..QH..F.WL.D...E..DY.G
Retrocopy LKAINVDLQSDAALQVDISDALSERDKVKFTVHTKSSLPNFKQNEFSVV*QHEEFIWLNDSFIENEDYVG

Parental  --IPPVPTRPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVSSHEVFLQRLASHPV-L
          ..IPP.P.RPDFD..REK.QKLGEGEG..TKEEF.KMKQELEAEYLA.FKKTV..HEVFL...A.HP..L
Retrocopy YIIPPAPPRPDFDASREKLQKLGEGEGLVTKEEFTKMKQELEAEYLAIFKKTVAMHEVFLCCVAAHPI<L

Parental  SKDRNFHVFLEYDQDLSVRRKNTKEMFGGFFKSVVKSADEVLFSGVKEVDDFFEQEKNFLINYYNKIKDS
          .KD.N.HVFLEY.QD.SV...........FFK..VKSAD.V..SGVK.VDDFFE.E..FL..Y.N..KD.
Retrocopy RKDLNLHVFLEYNQDWSV*XXXXXXXLEDFFKNMVKSADGVIVSGVKDVDDFFEHE*TFLLEYHN*VKDA

Parental  CAKADKMTRSHKNVADDYIHTAACLHSLALEEPTVIKT--LELHELFEKLRKVESRVSSDEDLKLTELXX
          .AK.D.MTRSHK..ADDY......L..L.....T.I....L...ELF.K.R..E.RVS.DEDLKL..L..
Retrocopy SAKSDRMTRSHKSAADDYNRIGSSLYALGTQDSTDICKFFLKVSELFDKTRQIEARVSVDEDLKLSDLLK

Parental  XXXXXXXXXXDLLYRRTKALIDYENSNKALDKARLKSRDVKLAEANQQECCQKFEQLSESAKEELISFKR
          ...........LLYRR...L.DYEN.NKALD.AR.K..DV..AE..QQ.CCQKFE..SESAK.ELI.FK.
Retrocopy YYLRESQASKELLYRRSRLLVDYENANKALDEARAKNKDVLQAETSQQLCCQKFEKISESAKQELIDFKT

Parental  KRVAAFRKNLIEMSELEIK
          .RVAAFRKNL.E..ELE.K
Retrocopy RRVAAFRKNLVELTELELK

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_1478 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 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000707	2 retrocopies	retro_chof_2390, retro_chof_265,
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478 , retro_chof_2166,
Callithrix jacchus	ENSCJAG00000004947	2 retrocopies	retro_cjac_2192, retro_cjac_3243,
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746, retro_mmul_832,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071,
Oryctolagus cuniculus	ENSOCUG00000017072	1 retrocopy	retro_ocun_1323,
Otolemur garnettii	ENSOGAG00000006157	1 retrocopy	retro_ogar_1203,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052, retro_ptro_717,
Sus scrofa	ENSSSCG00000007088	1 retrocopy	retro_sscr_593,
Ictidomys tridecemlineatus	ENSSTOG00000015416	1 retrocopy	retro_itri_1176,
Tursiops truncatus	ENSTTRG00000016432	1 retrocopy	retro_ttru_410,