RetrogeneDB ID: retro_chof_310

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_705:50701..51031(+)
• Located in intron of: ENSCHOG00000003822

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL12
• Ensembl ID: ENSCHOG00000006732
• Aliases: None
• Description: ribosomal protein L12 [Source:HGNC Symbol;Acc:10302]

Sequence

>retro_chof_310
AGGTGCACCAGGGGGAAAGTTGGTGCCACGTCTACTCTGGCCCCCGAGATCAGCTCTCAGGTCTGTCTTCAAAAAAGGTT
GATCAGGATATCATCAATGCAGCTGATAATTGGAAACGTCCAAGATTATGGTGAAACTGACCATTCAAAACAGAAAAGAC
CAGACTGAGGTAATTCCTTCTGCCTCCAACCTATCATCAAAGCCCTCAAGGAATCACCCAGAAACAGAAAGCAGCAGAAA
AACATTAAGCAGAGTGGAAATTTCACTTTTGATGAGATTGTCAATACTGCCTGACTGATGCAGTGTTGATCTTTAGGAAG
AAAATTCTCT

Alignment

ORF - retro_chof_310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.91 %
• Parental protein coverage: 98.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RCTGGEVGATSALAPKIGPL-GLSPKKVGDDIAKATGDWKGLR-ITVKLTIQNRQAQIEVVPSASAL-II
          RCT.G.VGATS.LAP.I....GLS.KKV..DI..A...WK..R.I.VKLTIQNR..Q.EV.PSAS.L.II
Retrocopy RCTRGKVGATSTLAPEISSQ<GLSSKKVDQDIINAADNWKRPR<IMVKLTIQNRKDQTEVIPSASNL<II

Parental  KALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELS
          KALKE.PR.RK.QKNIK.SGN.TFDEIVN.A..M...SL.R..S
Retrocopy KALKESPRNRKQQKNIKQSGNFTFDEIVNTA*LMQC*SLGRKFS

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_310 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 6 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006732	32 retrocopies	retro_chof_1081, retro_chof_129, retro_chof_145, retro_chof_1469, retro_chof_147, retro_chof_1531, retro_chof_156, retro_chof_1666, retro_chof_1724, retro_chof_1843, retro_chof_1886, retro_chof_197, retro_chof_1992, retro_chof_2080, retro_chof_2152, retro_chof_2169, retro_chof_2279, retro_chof_2318, retro_chof_249, retro_chof_2599, retro_chof_2614, retro_chof_2656, retro_chof_295, retro_chof_310 , retro_chof_354, retro_chof_386, retro_chof_484, retro_chof_592, retro_chof_677, retro_chof_831, retro_chof_916, retro_chof_925,
Latimeria chalumnae	ENSLACG00000015373	3 retrocopies	retro_lcha_31, retro_lcha_87, retro_lcha_92,
Loxodonta africana	ENSLAFG00000017669	10 retrocopies	retro_lafr_1, retro_lafr_193, retro_lafr_204, retro_lafr_286, retro_lafr_342, retro_lafr_41, retro_lafr_8, retro_lafr_802, retro_lafr_830, retro_lafr_984,
Macropus eugenii	ENSMEUG00000007380	12 retrocopies	retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Monodelphis domestica	ENSMODG00000004571	9 retrocopies	retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Rattus norvegicus	ENSRNOG00000016220	4 retrocopies	retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,