RetrogeneDB ID: retro_lafr_249

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:47328942..47329643(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADIPOR2
• Ensembl ID: ENSLAFG00000021355
• Aliases: None
• Description: None

Sequence

>retro_lafr_249
CACATCTCTTAGGCTGTGTATACTTCCTGTACCTGGGGATCTTTTATGTTTCTCCTAAACGTCTCCTTTGTGACACCTCT
GCAAGAGAAGGTGGTCTTTGGCTTATTCTTCTTGGGGGCAGTTCTCTGCCTTTCTTTTTTAGGTCTCTTCCACACAGTCT
AATACCACTCAGAGGGGGTCTCCTGGCTCTTCTCTGAACTGGCTACTCTGGTATTGCTCTTCTGATTATGGGAAGTTTTC
TTCCTTGGCTTTATTATTCTTCCAACAGTAATCCACAACCTTGTTTCATCTATTTGATTGTCATCTGTGTGCTGGGCATT
GCAGCTGTTATCATCCCAGTGGGACCGCATTTGCCACTCCTCAAGATCAGAGAGTAAGAGCAGGAGTGTTTGGGGGCCTA
GGCCTGAGTGGATCATTCCTATCATGTTGTATGTCATCTTGGAAGGATCCGTGAAAACTGCCACCTTAAGGCAGATAGGT
TGGTTGATGCCGATGGCCAGCTTCTGTATCAAGTGAGCTGCCCCGTATGCTGCCTGGATCCCCAAACGCATCTTTCCTGG
CAAGTGTGACGTCTCATTTCACTCTCATCAGCTGTTTGACAACTTTGTGGTTGCTGGAGCTTTCATTCGCTTCCATGGTG
TCTCAAACCTCAGGAATTCCCTTTCATGATTGGCGGGGGCTGCAGTGAAGAGAATGCTCTC

Alignment

ORF - retro_lafr_249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.71 %
• Parental protein coverage: 60.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HLLGCVFFLCLGIFYMFRPNISFVAPLQEKVVFGLFFLGAILCLSFSWLFHTVYCHSEGVSRLFSKL-DY
          H....V...C.....MF..N.SFV.PLQEKVVFGLFFLGA.LCLSF..LFHTV..HSEGVS.LFS.L..Y
Retrocopy HIS*AVYTSCTWGSFMFLLNVSFVTPLQEKVVFGLFFLGAVLCLSFLGLFHTV*YHSEGVSWLFSEL<GY

Parental  SGIALLIMGSFVPWLYYSFYCNPQPCFIYLIVICVLGIAAIIV-SQWDIFATPQYRGVRAGVFLGLGLSG
          SGIALLIMGSF.PWLYYS...NPQPCFIYLIVICVLGIAA.I.......FATPQ...VRAGVF.GLGLSG
Retrocopy SGIALLIMGSFLPWLYYSSNSNPQPCFIYLIVICVLGIAAVII<PSGTAFATPQDQRVRAGVFGGLGLSG

Parental  -IIPTLHYVISEGFLKAATIGQIGWLLLMASLYITGAALYAARIPERFFPGKCDIWFHSHQLFHIFVVAG
          .IIP...YVI.EG..K.AT..QIGWL..MAS..I..AA.YAA.IP.R.FPGKCD..FHSHQLF..FVVAG
Retrocopy <IIPIMLYVILEGSVKTATLRQIGWLMPMASFCIK*AAPYAAWIPKRIFPGKCDVSFHSHQLFDNFVVAG

Parental  AFVHFHGVSNL-QEFRFMIGGGCSEEDAL
          AF..FHGVSNL.QEF.FMIGGGCSEE.AL
Retrocopy AFIRFHGVSNL<QEFPFMIGGGCSEENAL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_249 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009050	1 retrocopy	retro_btau_320,
Choloepus hoffmanni	ENSCHOG00000012668	1 retrocopy	retro_chof_1133,
Callithrix jacchus	ENSCJAG00000000683	3 retrocopies	retro_cjac_2912, retro_cjac_3290, retro_cjac_504,
Loxodonta africana	ENSLAFG00000003520	1 retrocopy	retro_lafr_277,
Loxodonta africana	ENSLAFG00000021355	1 retrocopy	retro_lafr_249 ,
Microcebus murinus	ENSMICG00000005653	1 retrocopy	retro_mmur_818,
Myotis lucifugus	ENSMLUG00000002211	1 retrocopy	retro_mluc_66,