RetrogeneDB ID: retro_chof_1133

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_208490:61..727(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADIPOR2
• Ensembl ID: ENSCHOG00000012668
• Aliases: None
• Description: adiponectin receptor 2 [Source:HGNC Symbol;Acc:24041]

Sequence

>retro_chof_1133
GTGATATTACTCTTTTTGGGAATCTTGACCATGTTTAGACAAATGTGCATTTCAGGGCCTCTCTACAGAAGAAGAAGGTT
TAACAGATGTTCTTTTTGGATGCATTGCTCTGCCTTACTTTCTCCTGCCTCTTTCATACCATCTATTGTCGTTCACACAA
AATCTCTTGGACTTTTTTCTACTCTGGGATGGCTCTACTTATTATGGGAAACTTTGTCCCCTGCCTCTTTTATTCCTTCT
TCTGCTCCCCATAGCCAAGGCTCATCTACTTCTCCATCATTGTCTGTGTCCTGGGGATTCTTCCATCATTGTGGTGCACT
GGGAGCTGTTGGCCACCACTAAGCACCAGCAGACAAGAGCAGGAGTGTTCCTGTGACTTGGCGTGAGTGGTGGTGTGCCC
ACCATGCACATTACTTTTGCTGAGGGCTTTGTCAAAGCCACTGCCAGGAGCAGATGACTGGATCTTCCTCATGGCTGCAA
TGTACATCACTGCAGCTGCCCTTTATGCTACTTGAATCCCTGGGTACATCTGTCCTGGAAAGTTTGACATACGGTTCCAG
TCTCATTAGATTTTCCATGTCCTGGTGGGGACAGCTGCCTTTGTACACTTCTACAGAATATCCAACTTCAGGAATTCTGC
TATGTCTAGAAGGAGGCTGTACTGAT

Alignment

ORF - retro_chof_1133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.88 %
• Parental protein coverage: 59.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VFFLCLGIFYMFRP-NISFVAPLQEKVVFGLFFLGAILCLSFSWLFHTVYCHSEGVSRLFSKLDYSGIAL
          V..L.LGI..MFR..N..F.A.LQ.K.V...FFL.A.LCL.FS.LFHT.YC.S...S..F....YSG.AL
Retrocopy VILLFLGILTMFRQ<NVHFRASLQKKKV*QMFFLDALLCLTFSCLFHTIYCRSHKISWTFF---YSGMAL

Parental  LIMGSFVPWLYYSFYCNPQPCFIYL-IVICVLGI-AAIIVSQWDMFATPQYRGVRAGVFLGLGLSGIIPT
          LIMG.FVP.L.YSF.C.P.P..IY..I..CVLGI...IIV..W...AT......RAGVFL.LG.SG..PT
Retrocopy LIMGNFVPCLFYSFFCSP*PRLIYFSIIVCVLGI<SSIIVVHWELLATTKHQQTRAGVFL*LGVSGGVPT

Parental  LHYVISEGFLKAATI-GQIGWLMLMAGLYITGAALYAARIPERFFPGKCDIWFHSHQLFHIFVLAGAFVH
          .H....EGF.K.AT..G...W..LMA..YIT.AALYA..IP....PGK.DI.F.SH..FH..V...AFVH
Retrocopy MHITFAEGFVK-ATA>GADDWIFLMAAMYITAAALYAT*IPGYICPGKFDIRFQSH*IFHVLVGTAAFVH

Parental  FHGVSN-LQEFRFM-IGGGCSE
          F...SN.LQEF......GGC..
Retrocopy FYRISN<LQEFCYV<LEGGCTD

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_1133 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 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009050	1 retrocopy	retro_btau_320,
Choloepus hoffmanni	ENSCHOG00000006450	8 retrocopies	retro_chof_1127, retro_chof_1222, retro_chof_1917, retro_chof_2218, retro_chof_2380, retro_chof_471, retro_chof_749, retro_chof_995,
Choloepus hoffmanni	ENSCHOG00000012668	1 retrocopy	retro_chof_1133 ,
Loxodonta africana	ENSLAFG00000021355	1 retrocopy	retro_lafr_249,
Microcebus murinus	ENSMICG00000005653	1 retrocopy	retro_mmur_818,
Myotis lucifugus	ENSMLUG00000002211	1 retrocopy	retro_mluc_66,