RetrogeneDB ID: retro_chof_2398

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_71449:3741..4268(-)
• 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_2398
CAGATGGTTGACTTTTCCCTGGAGACATCCATCAAGGTCAAGGTTTTGAAAATTATGCCTGTGCAAATGCAGAACCATGC
TGGCTAATGGACCAGGGTTCAAGGCCTTTGTTGCCACGGGAACTACAATGGCCACAATGGTCTGGGTGTTAAGTGCTCCA
AGAAGGTAGTCACTATCATCCATGGGACCATTAGCCTGGACAAGCTCTGCATTGTCCCTGTGCAGCAGGACTGCTAGGAG
AACAAGAATGGTAAGTCCCACACTGTTACTTATAAGGCAACAGGATGCTGATTCTCTGTATTGGGGTCCCGCATCCCTGC
TCGCAGAGGCCCTATCATCATCTGGACCCCTATGCACAAAAAGCTGCTGCTGCTGCCTGATATTGATGATTACTACACCC
CAGCCAGGGGCTGCCTAGCCACCTGGGCAACTCTGCCAAGGCCACCACTGATACCATCTCCAAGAACTACAGATATGTCA
CCCCCAACCTCTGGGAAGAGATTGTGTCCACCAAGTCTACCTATCAG

Alignment

ORF - retro_chof_2398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.89 %
• Parental protein coverage: 87.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EIIDFFLETSLKDEVLKIMPVQKQTRAGQRTR-FKAFVAI-GDYNGHVGLGVKCSKEVATAIRGAIILAK
          ...DF.LETS.K..VLKIMPVQ.Q..AG..TR.FKAFVA..G.YNGH.GLGVKCSK.V.T.I.G.I.L.K
Retrocopy QMVDFSLETSIKVKVLKIMPVQMQNHAG*WTR>FKAFVAT<GNYNGHNGLGVKCSKKVVTIIHGTISLDK

Parental  LSIVPVRRGYWGNKIGKPHTVPCKVTVRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGC
          L.IVPV......NK.GK.HTV..K.T....SVL...IPA.RG..I...P..KKLL....IDD.YT.ARGC
Retrocopy LCIVPVQQDC*ENKNGKSHTVTYKATGC*FSVLGSRIPARRGPIIIWTPMHKKLLLLPDIDDYYTPARGC

Parental  TAT-LGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQ
          .AT.LGN.AKAT.D.ISK.Y.Y.TP.LW.E.V.TKS.YQ
Retrocopy LAT<LGNSAKATTDTISKNYRYVTPNLWEEIVSTKSTYQ

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_2398 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,