RetrogeneDB ID: retro_chof_155

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3519:3146..3915(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA1
• Ensembl ID: ENSCHOG00000005395
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 1 [Source:HGNC Symbol;Acc:9530]

Sequence

>retro_chof_155
AGAACCATGTTTTGCAACCAGTACAATAATGTCACTGTTTGGAGCCCTCAGGACAAGATTCGTCAAATTGAATATGCAAT
GGAAGCTGTCAAGCAAGGCTCAGCCACAGATGGGCTGAAATCGAAAACCCACGTAGTCTTGGTTGCATTGTAAAGGACGC
AATCAGAGCTTGCAGCCCATCAAAATAAAAATTCTCCATGTTGACAACCATGTTGGTATCTCAATTGTGGGGCTTATTGG
TGATGCTGGATTGTTATGTAATTTCATGCGCCAGGAGTGTTTGGATTCCAGATTTTTATTTGACAGACCCTTTCCTGTGC
CTTGTCTTGTATCTCTAATTGGAAGTAAGACCCTGATACCAACACAACAGTATGGCCAAAGACCATATGATTTGGGACGG
CTCATTGCTGTTTATGATGATATGGACCCTCATATTTTCCAAACCTGTCCATCTGGTAACTATTTTCACTGCAGAGCTAT
GTCCATTGGAGCCCATTCCCAGTCAGCTTGTACTTGCTTGGGAAGACATACATCTAAGTTTCTGGAGCATAATTTGAATG
AACTGATTAAACATGATCTGTATGCCTTAAGAGAGACACTTCCTGCAGAGCAGGACCTAACCACAAAGAAGGTTTCTTTT
GGAATTGTTGGCCAAGACTTGGAGTTTAAGATCTGTGATAACGATGATGTGTCTCCATTCCTGGGAGGTCTTGAAGAAAG
ACCACAGAGAAAGGCACAATCTGCTCAACCTTCTGATGAAACTGCAGAA

Alignment

ORF - retro_chof_155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.68 %
• Parental protein coverage: 95.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVKFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKK-ILHVD
          ...F.NQY.N.VTVWSPQ..I.QIEYAMEAVKQGSAT.GLKSKTH.VLVAL.R.QSELAAHQ.K.ILHVD
Retrocopy RTMFCNQYNN-VTVWSPQDKIRQIEYAMEAVKQGSATDGLKSKTHVVLVAL*RTQSELAAHQNK>ILHVD

Parental  NHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGY
          NH.GISI.GL..DA.LLCNFMRQECLDSRF.FDRP.PV..LVSLIGSKT.IPTQ.YG.RPY..G.LIA.Y
Retrocopy NHVGISIVGLIGDAGLLCNFMRQECLDSRFLFDRPFPVPCLVSLIGSKTLIPTQQYGQRPYDLGRLIAVY

Parental  DDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTT
          DDM.PHIFQTCPS.NYF.CRAMSIGA.SQSA.T.L.RH.S.F.E.NLNEL.KH.L.ALRETLPAEQDLTT
Retrocopy DDMDPHIFQTCPSGNYFHCRAMSIGAHSQSACTCLGRHTSKFLEHNLNELIKHDLYALRETLPAEQDLTT

Parental  KNVSIGIVGQDLEFTIYDDDDVSPFLEGLEERPQRKTQPAQPSEEPAE
          K.VS.GIVGQDLEF.I.D.DDVSPFL.GLEERPQRK.Q.AQPS.E.AE
Retrocopy KKVSFGIVGQDLEFKICDNDDVSPFLGGLEERPQRKAQSAQPSDETAE

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_155 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.

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002440	2 retrocopies	retro_amel_1733, retro_amel_1903,
Bos taurus	ENSBTAG00000006564	1 retrocopy	retro_btau_1833,
Choloepus hoffmanni	ENSCHOG00000005395	11 retrocopies	retro_chof_155 , retro_chof_1844, retro_chof_1991, retro_chof_2376, retro_chof_2626, retro_chof_267, retro_chof_2712, retro_chof_459, retro_chof_519, retro_chof_719, retro_chof_77,
Equus caballus	ENSECAG00000024086	1 retrocopy	retro_ecab_1078,
Felis catus	ENSFCAG00000011381	1 retrocopy	retro_fcat_972,
Homo sapiens	ENSG00000129084	1 retrocopy	retro_hsap_4720,
Gorilla gorilla	ENSGGOG00000001416	1 retrocopy	retro_ggor_2933,
Macropus eugenii	ENSMEUG00000011112	1 retrocopy	retro_meug_71,
Myotis lucifugus	ENSMLUG00000009251	4 retrocopies	retro_mluc_2444, retro_mluc_2445, retro_mluc_2463, retro_mluc_2515,
Macaca mulatta	ENSMMUG00000016446	1 retrocopy	retro_mmul_2509,
Mustela putorius furo	ENSMPUG00000013199	4 retrocopies	retro_mputfur_1243, retro_mputfur_224, retro_mputfur_338, retro_mputfur_825,
Mus musculus	ENSMUSG00000030751	1 retrocopy	retro_mmus_831,
Nomascus leucogenys	ENSNLEG00000017705	1 retrocopy	retro_nleu_1990,
Oryctolagus cuniculus	ENSOCUG00000000439	2 retrocopies	retro_ocun_1461, retro_ocun_1490,
Otolemur garnettii	ENSOGAG00000011622	3 retrocopies	retro_ogar_2267, retro_ogar_2644, retro_ogar_992,
Ochotona princeps	ENSOPRG00000013677	1 retrocopy	retro_opri_370,
Pongo abelii	ENSPPYG00000003466	2 retrocopies	retro_pabe_1883, retro_pabe_3664,
Pan troglodytes	ENSPTRG00000003385	1 retrocopy	retro_ptro_3137,
Sarcophilus harrisii	ENSSHAG00000015626	1 retrocopy	retro_shar_217,
Ictidomys tridecemlineatus	ENSSTOG00000006270	2 retrocopies	retro_itri_1470, retro_itri_987,
Tupaia belangeri	ENSTBEG00000012037	3 retrocopies	retro_tbel_2629, retro_tbel_323, retro_tbel_982,
Tarsius syrichta	ENSTSYG00000003869	2 retrocopies	retro_tsyr_1723, retro_tsyr_374,
Vicugna pacos	ENSVPAG00000008820	3 retrocopies	retro_vpac_344, retro_vpac_648, retro_vpac_82,