RetrogeneDB ID: retro_chof_1587

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_33249:9666..10379(-)
• 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_1587
AGCATTCTCAGCAGAGGCAGCAGCACCAGTTTTTGCTCTAGCTCTAGCTCCAGCTCTGACTCCAGCATCACCATGGGCTC
AGGTTATGGCAGCAGTGGTTCCAGCTCCTCTGAGGCCTCGAACCACTCATGAAGTTTCAGAACATCCCACAGGTCGAGCT
CTAGCAGCTCCTAGGATTCTCTGAGACCTTTCTGGCACAGACATAATAGGTAGCATTCTGCTCCAATTCCAAACCATCCA
AAAGAGATGAAAAGGAAAAAGAGACCTTTCTCTAAACCCACCAAAGTACACATTGGAAGGCTCACCTGGAATGTGACCAA
GGATCAAATCATGGAGATATTTTCCACCTATGGGAAAATTTAAATGATTGACAAGGCCATAGAAAGGACGCATCCTCATG
TATCCAAAATCTATGCCTATGTTGAGTTTGAGAATCTGGATGAAGCCGAGAAGGCACTGAAACACATGAACGGAAGACTA
ATAGATGGCCAGGAGATCGCTGCTCCAGCTATGCTGGCCCCTGGCCTCCACCACCCTGCATGCAATTCAGCCATCCCATC
AGAATGTGGCCACTACATCCCAGATGGTACAGAGGTCACCCCCATGGATGAGGAGAAGATCCTGCTCTTCAAGACACAGG
TCTCCTGTGTGCTGGCAATCTAGTCCCCTGGCTGCTGCCACCACAAAAGCCCTCCAGCTCCAACTCCTCACAA

Alignment

ORF - retro_chof_1587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.79 %
• Parental protein coverage: 78.88 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SASSGSSSTRSRSSSTSSSGSSTSTGSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRR
          S..S..SST...SSS.SSS.SS...GS..GSS.SS.S..S..S...R.S..SSSS.S....R.......R
Retrocopy SILSRGSSTSFCSSSSSSSDSSITMGSGYGSSGSSSSEASNHS*SFRTSHRSSSSSS*DSLRPFWHRHNR

Parental  SRSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYA
          ..S...P....E..RK.R.P..KPTKVHIGRLT.NVTKD.IMEIFSTYGKI.MID...ER.HPH.SK.YA
Retrocopy *HSAPIPNHPKEMKRKKR-PFSKPTKVHIGRLTWNVTKDQIMEIFSTYGKI*MIDKAIERTHPHVSKIYA

Parental  YVEFENPDEAEKALKHMDGGQIDGQEITATAVLA-PWPRPPPRRFSPPRRMLPPPPMWRRSPPR-MRRR-
          YVEFEN.DEAEKALKHM.G..IDGQEI.A.A.LA.PWP.PP...FS.P.RM.P..P.W.R..P....RR.
Retrocopy YVEFENLDEAEKALKHMNGRLIDGQEIAAPAMLA<PWPPPPCMQFSHPIRMWPLHPRWYRGHPH<WMRRR

Parental  SRSPRRRSPVRRRSR-SPGRRRHRS-RSSSNSSR
          S.S.R.RSPV...S..SPG...H.S..SSSNSS.
Retrocopy SCSSRHRSPVCWQSS<SPGCCHHKS<PSSSNSSQ

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_1587 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,