RetrogeneDB ID: retro_chof_2607

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_89966:5385..5827(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSCHOG00000012360
• Aliases: None
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_chof_2607
CTGGGAGTTGAGTGCTCCAAGGAAGTAGGCACCACCATCCACGGGGCCATCATTGTGGCCAAGCTGTCCATCATCCCTGT
GTGCTGGGACTAATGTGGGAACAAGGTCAGCAAGTCCCACACCTTCCCATGCAAGGTGGCAGGACACTGGGACTCCATGC
TTGTGTGTCTCATCCATGTCCCCAGGGGCACTGGCATTGTCTCAACCTCCAAGCCCAAGAAATTTTTGCTGGTGGTGGTA
TTGACCACTGTTATATCTGGCCAGGGCCTGCACAGCACATTGGGAAAATTGCCTAAAGCCACCTTGATACCATCTCCAAG
ACCAGCAGCTATCTTTCTCCCAACCTCTGCAAAAAACCTTGATCACCAAGTCTCTGTCTCAGGAGTTCACTCTCCATCTT
GTAAAGACCCACACCAGAGTCTCCATGCAGAGGATACAGGCC

Alignment

ORF - retro_chof_2607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.99 %
• Parental protein coverage: 73.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTVRCGSVLVRLIPAPRGTGIVSAP
          LGV.CSKEV.T.I.GAII.AKLSI.PV.....GNK..K.HT.PCKV.....S.LV.LI..PRGTGIVS..
Retrocopy LGVECSKEVGTTIHGAIIVAKLSIIPVCWD*CGNKVSKSHTFPCKVAGHWDSMLVCLIHVPRGTGIVSTS

Parental  VPKKLLMM-AGIDDCYT-SARGCTA-TLGNFAKAT-FDAISKTYSYLTPDLWK-ETVFTKSPYQEFTDHL
          .PKK.L....GID.CY...AR.CTA.TLG...KAT..D.ISKT.SYL.P.L.K..T..TKS..QEFT.HL
Retrocopy KPKKFLLV<GGIDHCYI<LARACTA<TLGKLPKAT<LDTISKTSSYLSPNLCK<KTLITKSLSQEFTLHL

Parental  VKTHTRVSVQRTQA
          VKTHTRVS.QR.QA
Retrocopy VKTHTRVSMQRIQA

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_2607 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 5 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Choloepus hoffmanni	ENSCHOG00000012360	9 retrocopies	retro_chof_1056, retro_chof_2398, retro_chof_2545, retro_chof_2607 , retro_chof_368, retro_chof_378, retro_chof_535, retro_chof_919, retro_chof_989,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Sus scrofa	ENSSSCG00000022859	8 retrocopies	retro_sscr_280, retro_sscr_293, retro_sscr_412, retro_sscr_486, retro_sscr_729, retro_sscr_803, retro_sscr_950, retro_sscr_951,