RetrogeneDB ID: retro_lafr_1200

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_88:2589127..2589689(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VBP1
• Ensembl ID: ENSLAFG00000016507
• Aliases: None
• Description: None

Sequence

>retro_lafr_1200
ATGGCGGCTGCTAAGGGTGGCCACTGACTTCAGATAAGTGGCCACGGGACCAGGCGGCGGCTCCACCGGGGGATTCCCAT
GGCCGTGTTTGTGGAAGACGTAGATTCCTTCATGACACAGCCTGGGAATGAGACTGAAGATACGGTAGTAAGAAGTTGGA
TGAACAACACCAGAAGTATAAGTTCTGGTGGAACTCAATCTTGCTCAAAAGAAAAGGAGGCTAAAAGGTCAGATTCCAGA
TATTAAGCAGACTTTAGAAATTCTTAAGTCCATGCCGAAGAAAAAAAGAGTCCACCAATTCACTGGAGACCAGATTCTTA
TTGGCAGATAACCTGTACTTTACAGCTTCGGTTCCCCTACGGATGCAGTGTGCTGTGGCTGGGGGCTGAGGGAGTGCTTG
AAGATGATCCCGATGAGGCCCAGACCTTGGCGCGCAAGAACCTACCAGCGGCCGCAAAGAATCTTGATTCTATTAAGACG
TTGACTTTCTTCCAGGTCAATTTACTGCCACAGAATCAATACGGCCAGCGTTCGTAATTGGGATGTAAAAAGAAGAAACA
AA

Alignment

ORF - retro_lafr_1200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.53 %
• Parental protein coverage: 95.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MAAAKDGCGLGEVATGNGRRLHLGIPEAVFVEDVDSFMKQPGNETADVVL-KKLDEQYQKYKFMELNLAQ
          MAAAK.G..L.....G..RRLH.GIP.AVFVEDVDSFM.QPGNET.D.V..KKLDEQ.QKYKF.......
Retrocopy MAAAKGGH*LQISGHGTRRRLHRGIPMAVFVEDVDSFMTQPGNETEDTVV<KKLDEQHQKYKFWWNSILL

Parental  K-KRR-LKGQIPEIKQTLEILKYMQK-KKESTNSLETRFLLADNLYCKASVP-PTDKVC-LWLGANVMLE
          K.K.R.LKGQIP.IKQTLEILK.M.K.KKESTNSLETRFLLADNLY..ASVP.PTD.VC.LWLGA...LE
Retrocopy K<KKRRLKGQIPDIKQTLEILKSMPK>KKESTNSLETRFLLADNLYFTASVP<PTDAVC<LWLGAEGVLE

Parental  YDIDEAQALLEKNLSTATKNLDSLEEDLDF-LRDQFTTTE-VNMARVYNWDVKRRNK
          .D.DEAQ.L..KNL..A.KNLDS....L.F.L..QFT.TE..N.A.V.NWDVKRRNK
Retrocopy DDPDEAQTLARKNLPAAAKNLDSI-KTLTF<LPGQFTATE<INTASVRNWDVKRRNK

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_1200 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013652	1 retrocopy	retro_cpor_466,
Echinops telfairi	ENSETEG00000017655	2 retrocopies	retro_etel_2085, retro_etel_552,
Latimeria chalumnae	ENSLACG00000016144	1 retrocopy	retro_lcha_18,
Loxodonta africana	ENSLAFG00000016507	2 retrocopies	retro_lafr_1200 , retro_lafr_163,
Myotis lucifugus	ENSMLUG00000015396	3 retrocopies	retro_mluc_1600, retro_mluc_2019, retro_mluc_986,
Macaca mulatta	ENSMMUG00000015095	1 retrocopy	retro_mmul_124,
Oryctolagus cuniculus	ENSOCUG00000017448	2 retrocopies	retro_ocun_233, retro_ocun_747,
Sarcophilus harrisii	ENSSHAG00000002823	1 retrocopy	retro_shar_7,