RetrogeneDB ID: retro_lafr_789

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_39:1332218..1332817(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19ORF40
• Ensembl ID: ENSLAFG00000006401
• Aliases: None
• Description: None

Sequence

>retro_lafr_789
GACACAGGCCCCATACATGTGCCTTTTGGGCACACTGTGGCCAGTGAGAAATAGCGTGGGTCACAGCTGGTGCAGGGGAT
GCAAGGGAAAATTAAACTCACTTTTGAGGATCACCTGACACCTGTAGATTTTCACTTGGCTAACAGATCCTGTATTCTTT
ATATCACCGAAGCTGATTTGGTGGCAGGAAATGGCTACAGAAATAGGCTTGCTCAGGTTAGAAATTCCAGTAATCTTCTA
CTAGTTGAAAAGACACAGATGATTAGATGATACATCCCAGCTGTACAGAATTTTACTGTGCTGGACCTTGGGATGCTGTT
GCTTCCAGTGGCCAGCCAGATGGACGCGTCCTGCCTCCTTATTCAGTTAGTCCAAGAACCAACCAAAGAGCCCAGTAAGA
ACACTTTTCTCAGGAAGACACATGCTCTGCTCTGTAAGCCATCCCTCCTTCAAACTGTGCAGCAGATCCCAGGAGTTGGA
AAATAAAAGCTCCCCTTCTGCTTCAGAAATTCCCAAGTATTCAACAATTAAATAACGCATCCATCCAAAAACCAGAGCGA
GTTGTTAGACAAGCAGTAGCACAGCAAATTCACGTTTTT

Alignment

ORF - retro_lafr_789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 95.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DTGPIHVPFGYVVASEKWRGSELAQGLQGKIKLLFEDCLTPVDFYLSSRSCVLYITEADLVAGNGYRKRL
          DTGPIHVPFG..VASEK.RGS.L.QG.QGKIKL.FED.LTPVDF.L..RSC.LYITEADLVAGNGYR.RL
Retrocopy DTGPIHVPFGHTVASEK*RGSQLVQGMQGKIKLTFEDHLTPVDFHLANRSCILYITEADLVAGNGYRNRL

Parental  VRVRNSSNLQGIILVEKTQMSEQYFPAVQKFTVLDLGMVLLPVASQMEASRLIIQLVQEQTKEPSKNPFV
          ..VRNSSNL....LVEKTQM...Y.PAVQ.FTVLDLGM.LLPVASQM.AS.L.IQLVQE.TKEPSKN.F.
Retrocopy AQVRNSSNL---LLVEKTQMIR*YIPAVQNFTVLDLGMLLLPVASQMDASCLLIQLVQEPTKEPSKNTFL

Parental  RKKCTVLSEPSLLRTVQQIPGVG-KVKAPLLLQKFPSIQELSNASIHELEQVVGQAVAQQIHTF
          RK....L..PSLL.TVQQIPGVG.K.KAPLLLQKFPSIQ.L.NASI...E.VV.QAVAQQIH.F
Retrocopy RKTHALLCKPSLLQTVQQIPGVG<KIKAPLLLQKFPSIQQLNNASIQKPERVVRQAVAQQIHVF

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_789 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000728	2 retrocopies	retro_cjac_1011, retro_cjac_3952,
Cavia porcellus	ENSCPOG00000011965	1 retrocopy	retro_cpor_1536,
Dasypus novemcinctus	ENSDNOG00000014134	4 retrocopies	retro_dnov_1817, retro_dnov_2382, retro_dnov_426, retro_dnov_942,
Echinops telfairi	ENSETEG00000002716	1 retrocopy	retro_etel_458,
Loxodonta africana	ENSLAFG00000006401	4 retrocopies	retro_lafr_165, retro_lafr_365, retro_lafr_415, retro_lafr_789 ,
Myotis lucifugus	ENSMLUG00000013287	1 retrocopy	retro_mluc_522,
Macaca mulatta	ENSMMUG00000017939	1 retrocopy	retro_mmul_788,
Procavia capensis	ENSPCAG00000009727	1 retrocopy	retro_pcap_444,
Sarcophilus harrisii	ENSSHAG00000016372	1 retrocopy	retro_shar_299,