RetrogeneDB ID: retro_chof_493

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_114430:3746..4218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSCHOG00000004866
• Aliases: None
• Description: RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]

Sequence

>retro_chof_493
CGCTCCGCAGCCCGGAGGGCTCCTCCTACCAAACGCACAGACCGCTCTGAGGAGAAGTCCAAGGATTGCTCTGAAGGTCA
AAGGGGCCACCAAGGAGGCAAGCGAGAAGTATCGTTGCAGGGGTAAAACCCGACAGAGGCGTGGCGCTTCCAGAGGCCGC
AGCAGCACCAGGTCTCGCTCTAGCGCCAGCTCCAGCGCCGGCTCCAGTACTGGCACCGGCTCAAGCAGTGGTCCCAGCTC
CTCCTCGGTGTCGAGCCGCTCGGGAGGTTCCAGCACAGCCCGCAGCTCCAGCTGCAGCACCTCCTCGGGCTCTCCGAGTC
CTCGGCGCAGACACGACGACAGACGGTGTTCCCGCTCCACATACCACCCAGAAGAGATGGAAAGGAAGGAAAAACACGGA
GTCCTTCCCTAAACCCGCCGAAGTGCACCCGGGAGGCTCACCCGGAATGGGAGCAGGGATCACATCAGGGAG

Alignment

ORF - retro_chof_493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.58 %
• Parental protein coverage: 52.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSSTRAPSPSKRKERSDEKSKDRS-KDKGATKD--EKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGSS
          .S..R...P.KR..RS.EKSKD.S.K.KGATK...EK.R.R.KTR.RR.AS.G.SSTRSRSS..SS.GSS
Retrocopy RSAARRAPPTKRTDRSEEKSKDCS>KVKGATKEASEKYRCRGKTRQRRGASRGRSSTRSRSSASSSAGSS

Parental  TSTGSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKER-KRRSPS
          T.TGSSSG.SSSS.SSRSG.SST.RSSS.S.SSGSPSP.RRRHD.RR.SRS...P.....KE......P.
Retrocopy TGTGSSSGPSSSSVSSRSGGSSTARSSSCSTSSGSPSP-RRRHDDRRCSRSTYHPEEMERKEK>TESFPK

Parental  PKPTKVHIG-RLTRNVTKDHIME
          P....VH.G.RLTRN...DHI.E
Retrocopy P--AEVHPG<RLTRNGSRDHIRE

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_493 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004866	4 retrocopies	retro_chof_1587, retro_chof_1985, retro_chof_2272, retro_chof_493 ,
Cavia porcellus	ENSCPOG00000002066	2 retrocopies	retro_cpor_363, retro_cpor_953,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Pan troglodytes	ENSPTRG00000031310	1 retrocopy	retro_ptro_1967,
Pteropus vampyrus	ENSPVAG00000005105	1 retrocopy	retro_pvam_296,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,