RetrogeneDB ID: retro_chof_410

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_105064:3920..4281(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SARNP
• Ensembl ID: ENSCHOG00000005081
• Aliases: None
• Description: SAP domain containing ribonucleoprotein [Source:HGNC Symbol;Acc:24432]

Sequence

>retro_chof_410
CTGTCAGCAGAGAAGCACGTGGTAAAAATTACACATGAAATAACACAGACTGAAAGAATGCAGAAGAGAGCTGAACAATT
CAACGTACCTGTGAGCTCGGAGGGTAAGAAAGCTGCCTGAGCAGTTAGGTTTCACATTTCTTTGGTTCCAACAAAAGGCC
TGTCATCTGACACCAAAACTATGGCTAAGCTGGATAAGCTGAAGGAAAGAGCTCAAAGATTTGCTTTGAATGTTTCTTCA
ATCTCCAGACAGCCTGAAGATGACGAGAAGCTGAAAGAGGAAGGAGCGATTCGGGACTGTCACAAGTTCAGCGGGAACTG
AAACCACAGAGGATACAGAGGCAAAGAAGAGGAAAGGAGCT

Alignment

ORF - retro_chof_410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.67 %
• Parental protein coverage: 61.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSAEKKVVKITSEIPHTERMQKRAERFNVPVSLESKKAARAARFGISSVPTKXXXXXXXXXVNLDKLKER
          .SAEK.VVKIT.EI..TERMQKRAE.FNVPVS.E.KKAA.A.RF.IS.VPTK...........LDKLKER
Retrocopy LSAEKHVVKITHEITQTERMQKRAEQFNVPVSSEGKKAA*AVRFHISLVPTKGLSSDTKTMAKLDKLKER

Parental  AQRFGLNVSSISRKSEDDEKLKK-RKERFGIVTSSAGTGTTEDTEAKKRKRA
          AQRF.LNVSSIS.....D....K.RKERFG.VTSSAGT.TTEDTEAKKRK.A
Retrocopy AQRFALNVSSIS-RQPEDDEKLK>RKERFGTVTSSAGTETTEDTEAKKRKGA

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_410 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011769	2 retrocopies	retro_amel_1602, retro_amel_347,
Bos taurus	ENSBTAG00000020662	1 retrocopy	retro_btau_202,
Choloepus hoffmanni	ENSCHOG00000005081	5 retrocopies	retro_chof_1001, retro_chof_1749, retro_chof_410 , retro_chof_705, retro_chof_93,
Cavia porcellus	ENSCPOG00000011755	1 retrocopy	retro_cpor_1313,
Erinaceus europaeus	ENSEEUG00000015176	1 retrocopy	retro_eeur_549,
Loxodonta africana	ENSLAFG00000015053	1 retrocopy	retro_lafr_1024,
Myotis lucifugus	ENSMLUG00000003565	2 retrocopies	retro_mluc_1915, retro_mluc_484,
Monodelphis domestica	ENSMODG00000028949	1 retrocopy	retro_mdom_1909,
Mustela putorius furo	ENSMPUG00000000885	1 retrocopy	retro_mputfur_617,
Mus musculus	ENSMUSG00000078427	1 retrocopy	retro_mmus_54,
Otolemur garnettii	ENSOGAG00000001693	3 retrocopies	retro_ogar_1630, retro_ogar_2272, retro_ogar_2333,
Procavia capensis	ENSPCAG00000009477	2 retrocopies	retro_pcap_262, retro_pcap_45,