RetrogeneDB ID: retro_chof_2465

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_78114:7306..8022(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSCHOG00000007238
• Aliases: None
• Description: ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]

Sequence

>retro_chof_2465
GTTGATCCATTTTCTAAGAAAGAGTGATATGATGTGAAAGCACCAGCAATGTTTAATATAAGAATATTGGAAAAACACTA
GTTACAAGGACTCAAGAAACCAAAATTTCATCTGATGGCCTTAAGGGTCATGTTTTTGAAGTGAGCCTTGCTGATCTGCA
GAACGATGAAGTTGCATTTAGAAAATTCAAGCTAATTATTGAGGATGTGCAGGGCAAAAACTGCCTAACCAACTTCCATG
GCATGGATCTTACCCATGACAAAGTGTGTTCCATGGTCAAAAAATGGCAGACCATGATTGAAGCTCATGTCGATGTCAAA
ACTACCAATGGTTATTTGCTTTGTCTGTTCTGTGTTGGTTTTACCAAAAAATGCAACAGTCAGATTTGGAAGACCTCTTA
TGCTCAGCACCAAATCTGGAAGAAGATGATGGAAATCATGACCTGAGAAGTGCAGACAAATGACTTGAAAGAAGTGGTCT
ACAAATTGATTCCAGACAGCATTGGTGAAGACATAGAGAAGGCTTGCCAGTCGATCTATCCTCTCCATGATGTGTTTGTG
AGAAAAGTAAAAATGCTGAAGAAGCCCAAGTTTGAATTGGGAAAACTCATGGAGCTTCATGGTGAAGGTAGTAGTTCTGG
AAAAGCAACTGGAGATGAGATGGGTGCTAAAGTGTAATGAGCTGATGGTTATGAGCCACCAGTCCAAGAATCTGTT

Alignment

ORF - retro_chof_2465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDPFSKKDWYDVKAPAMFNIR-NIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITED
          VDPFSKK..YDVKAPAMFNIR.NIGKTLVTRTQ.TKI.SDGLKG.VFEVSLADLQNDEVAFRKFKLI.ED
Retrocopy VDPFSKKE*YDVKAPAMFNIR<NIGKTLVTRTQETKISSDGLKGHVFEVSLADLQNDEVAFRKFKLIIED

Parental  VQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQ
          VQGKNCLTNFHGMDLT.DK.CSMVKKWQTMIEAHVDVKTT.GYLL.LFCVGFTKK.N.QI.KTSYAQHQ.
Retrocopy VQGKNCLTNFHGMDLTHDKVCSMVKKWQTMIEAHVDVKTTNGYLLCLFCVGFTKKCNSQIWKTSYAQHQ-

Parental  VRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLME
          ...I.KKMMEIMT.EVQTNDLKEVV.KLIPDSIG.DIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLME
Retrocopy ---IWKKMMEIMT*EVQTNDLKEVVYKLIPDSIGEDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLME

Parental  LHGEGSSSGKATGDETGAKVERADGYEPPVQESV
          LHGEGSSSGKATGDE.GAKV..ADGYEPPVQESV
Retrocopy LHGEGSSSGKATGDEMGAKV**ADGYEPPVQESV

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_2465 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 7 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007238	34 retrocopies	retro_chof_1076, retro_chof_1092, retro_chof_1207, retro_chof_126, retro_chof_1309, retro_chof_1311, retro_chof_1341, retro_chof_1362, retro_chof_1377, retro_chof_1393, retro_chof_1395, retro_chof_1441, retro_chof_1488, retro_chof_1490, retro_chof_1598, retro_chof_1626, retro_chof_2056, retro_chof_2179, retro_chof_220, retro_chof_2201, retro_chof_2282, retro_chof_2417, retro_chof_2465 , retro_chof_2500, retro_chof_2613, retro_chof_2628, retro_chof_2635, retro_chof_2668, retro_chof_342, retro_chof_370, retro_chof_685, retro_chof_824, retro_chof_826, retro_chof_912,
Macaca mulatta	ENSMMUG00000021821	1 retrocopy	retro_mmul_2297,
Monodelphis domestica	ENSMODG00000000969	6 retrocopies	retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mus musculus	ENSMUSG00000028081	2 retrocopies	retro_mmus_218, retro_mmus_254,
Rattus norvegicus	ENSRNOG00000011893	1 retrocopy	retro_rnor_198,
Sarcophilus harrisii	ENSSHAG00000015088	2 retrocopies	retro_shar_777, retro_shar_95,
Tursiops truncatus	ENSTTRG00000013094	10 retrocopies	retro_ttru_101, retro_ttru_1014, retro_ttru_1456, retro_ttru_170, retro_ttru_1789, retro_ttru_1945, retro_ttru_263, retro_ttru_319, retro_ttru_779, retro_ttru_940,