RetrogeneDB ID: retro_chof_368

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_100592:370..825(-)
• 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_368
CACCAGGGACTGGGTGTGAAGTGCTCCAAGGAGGTAGCCACCGCCATGCATGTGGCAGTATCCCAGCCACGCTCTCCTTT
GTCCCTGTGTGGCAGGGCTACTGGGGTCCCAGACCAGCGAGCCCCATGCTGTCCCTTGCAAGGTGACCGGATGCTGTGGC
TCTGGGCTGAGCGCCTCATCCCCACAGCCAATGGCACTGACAGTGTCTTGGCCCCAGTGCCCAAGAAGCTGCTGCTGACG
GCCAGTATTGACCATGGCTGCACCTGGGCCAGGGGCTGCATGACCACCCAGGCAACTTCTCCAAGTCCACCTTCGAAGTC
ATCTCCAAGAACTATAGCTATCTCACTCCCCACCTCTAGAAAGAGACCGAGTTTACCAAGTCTCCCTCTCAAGAGTTCAC
CTGCCATCTTGTCAAGGCCCACATCAGAGTCTTCATGCAGAGATCCTAGACCCCA

Alignment

ORF - retro_chof_368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.69 %
• Parental protein coverage: 75.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HVGLGVKCSKEVATAIRGAI-ILAKLSIVPVRRGYWG-NKIGKPHTVPCKVTVRCGSVLV-RLIPAPRGT
          H.GLGVKCSKEVATA...A..I.A.LS.VPV..GYWG......PH.VPCKVT..CGS.L..RLIP...GT
Retrocopy HQGLGVKCSKEVATAMHVAV<IPATLSFVPVWQGYWG<SQTSEPHAVPCKVTGCCGSGLS<RLIPTANGT

Parental  GIVSAPVPKKLLMMAGIDDCYTSARGCTATL-GNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTD
          ..V.APVPKKLL..A.ID...T.ARGC..T..GNF.K.TF..ISK.YSYLTP.L.KET.FTKSP.QEFT.
Retrocopy DSVLAPVPKKLLLTASIDHGCTWARGCMTTQ<GNFSKSTFEVISKNYSYLTPHL*KETEFTKSPSQEFTC

Parental  HLVKTHTRVSVQRTQAP
          HLVK.H.RV..QR...P
Retrocopy HLVKAHIRVFMQRS*TP

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_368 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,