RetrogeneDB ID: retro_chof_1985

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_444063:299..885(+)
• 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_1985
GGGCTCAAGTGTGGTGCCAGCTCCTCTTCCGCCTCCAGCTCGGGAAGTTCCAGCACATCCTGCAGCTCCAGCTCCAGCAG
CTCCTCGGACTCTCCAAGTCCTTCTCGGCGCAGACACGACAAGGTGGTGTTCCCACTCCAAATCCAAACCACCCAAAAGA
GATGACAAGGAAAGAAAAAGGCAGAGTCCTTCCCCTAAACCCACCAAAGTGCACACTGGGAAGGCTCACCCGGAATGTGA
CCACAAATCATATCATGGAGTTATTTTCTACCTATGGGAAATTTAAAATGATTGGCATGCCTGTGGAAAGGATGCAGTCC
ATCTTTCCAACGGCTACGCCTGTGTTGAGATTGAGAATCCGGATGAAGCAGAGAAGGCGCTGAAACACAAGATTGGAGGA
CAAATAGCTGGCCAGGAGCTCGTTGCCACAGCTGTGCTGCCCCCCCCCCCCGGCCTTGGCCATCCACCCAGGCCGTTCAG
CCCTCCCAGGAGAATGCTGCCACCACCTCCCATGTGGCACAGGTCACCCCCACGGATGAGGAGACCCCAGGCGCAGGCTC
CTGTGCGCTGGCGCTCCTGGTCCCCT

Alignment

ORF - retro_chof_1985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.57 %
• Parental protein coverage: 65.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDN-RRRSRSKSKPPKRDEKERKRRSPSPKP
          G...G.SSSSASS.SGSSSTS.SSSSSSSS.SPSPS.RR....R..S.SKSKPPKRD.KERKR.SPSPKP
Retrocopy GLKCGASSSSASS-SGSSSTSCSSSSSSSSDSPSPS-RRRHD>RWCSHSKSKPPKRDDKERKRQSPSPKP

Parental  TKVH-IGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHP-HLSKGYAYVEFENPDEAEKALKHMDGGQI
          TKVH..GRLTRNVT..HIME.FSTYGK.KMI.MPVERM...HLS.GYA.VE.ENPDEAEKALKH..GGQI
Retrocopy TKVH>LGRLTRNVTTNHIMELFSTYGKFKMIGMPVERMQS<HLSNGYACVEIENPDEAEKALKHKIGGQI

Parental  DGQEI--TATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSP
          .GQE...TA..........PPR.FSPPRRMLPPPPMW.RSPPRMRR....P....PVR.RS.SP
Retrocopy AGQELVATAVLXXXXGLGHPPRPFSPPRRMLPPPPMWHRSPPRMRR----PQAQAPVRWRSWSP

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_1985 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,