RetrogeneDB ID: retro_chof_566

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_122164:4079..4601(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM97
• Ensembl ID: ENSCHOG00000011105
• Aliases: None
• Description: transmembrane protein 97 [Source:HGNC Symbol;Acc:28106]

Sequence

>retro_chof_566
ATGGGGATACTGGGCTTTGGGCATGGCCTGGAGTGGCTGCTGGGCTTCAACTTCCTCTCCCACATCCCCATCACCTTGTT
GATGGACCAGTGGGTGGTGCTGCCCTGCAAATTCTAACCAGCAGAGCTGAGAAACCTGCTGAATTGATATGTTACGGAGT
TCAAAGACCCTCTGCTAGAGGATCCTACAACTCGGTTTAAGTCCTTCCTGTTTTGGAGCTGTGTTTCAGCAGTCTTTCTT
TCCCATACTGACATATGCCTTCTTCAAAGAGGGCTGCAAATGAATCCACACTCCTGTGATCATCTACTCAGTTCACAGCA
TAAAACTTTAATTTCAATTATTTTCAAATTTCTATTTGAGAAGTTCTCTAAAGCCAGTGGTTTCAAAGGACAAGGACCTA
AGATTTTCCATGAAAAACTAAACCTTGTTTTTGTCTATGCCCCCTACTTTCTCATCCCTTTCATGCTTCTGCTTTTCATG
TTGTGGAGCCCCTACTATAAGTATGAGGAGAAAAAATTAAAA

Alignment

ORF - retro_chof_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.22 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGVLGFRRGLEWLLGFFFLSHIPITLFIDLQVVLPRELYPVELRNLLNWYTKEFKDPLLQDPPTWFKSFL
          MG.LGF..GLEWLLGF.FLSHIPITL..D..VVLP....P.ELRNLLN.Y..EFKDPLL.DP.T.FKSFL
Retrocopy MGILGFGHGLEWLLGFNFLSHIPITLLMDQWVVLPCKF*PAELRNLLN*YVTEFKDPLLEDPTTRFKSFL

Parental  F-CELVF-QLPFFPIATYAFFKGGCKWIRTPAIIYSVHLITI-LIPILSELLFGEFSKASGFKGQGPKTF
          F..EL.F.Q..FFPI.TYAFFK.GCK.I.TP.IIYSVH.I...LI.I....LF..FSKASGFKGQGPK.F
Retrocopy F<LELCF<QQSFFPILTYAFFKEGCK*IHTPVIIYSVHSIKL<LISIIFKFLFEKFSKASGFKGQGPKIF

Parental  RERLTLVSFYAPYFLIPLMLLLFMWQSPYYTYEEKRKK
          .E.L.LV..YAPYFLIP.MLLLFM..SPYY.YEEK..K
Retrocopy HEKLNLVFVYAPYFLIPFMLLLFMLWSPYYKYEEKKLK

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_566 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011105	1 retrocopy	retro_chof_566 ,
Homo sapiens	ENSG00000109084	1 retrocopy	retro_hsap_4027,
Gorilla gorilla	ENSGGOG00000004565	1 retrocopy	retro_ggor_2703,
Macaca mulatta	ENSMMUG00000019142	1 retrocopy	retro_mmul_2323,
Mus musculus	ENSMUSG00000037278	1 retrocopy	retro_mmus_1451,
Nomascus leucogenys	ENSNLEG00000001868	1 retrocopy	retro_nleu_1574,
Otolemur garnettii	ENSOGAG00000003329	1 retrocopy	retro_ogar_1913,
Pongo abelii	ENSPPYG00000008086	1 retrocopy	retro_pabe_3307,
Pan troglodytes	ENSPTRG00000008909	1 retrocopy	retro_ptro_2731,
Ictidomys tridecemlineatus	ENSSTOG00000007542	2 retrocopies	retro_itri_341, retro_itri_758,
Tupaia belangeri	ENSTBEG00000005125	2 retrocopies	retro_tbel_2160, retro_tbel_2221,