RetrogeneDB ID: retro_lafr_813

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:46110738..46111124(+)
• Located in intron of: ENSLAFG00000001980

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000008170
• Aliases: None
• Description: None

Sequence

>retro_lafr_813
ATGACAGATTATAGAGATGAGCAGCTCAACAAGTTGGAGTCTCTAGAATCTGATTTTTTCACGGCGTTATCAGAAAATTC
ACCCAGGTTTGCCATTACTGTGACACCTGAAGCTGGGAAAAATGATGAAACTGCCCAGATTACACTCAAGTTTAGGTACA
ATGAAAAACAACCAGATGAAGCTCCCCTTTATGAAATATTCTCCCAAGAAAATCTAGCAGATAATGAGATCTCAGGTGAT
TCAAAAGTTTTAGCATTACAGGCAGAAGGAAACCTTGGTCTGGTAATAAGCTTTACTTTAGTGTCAGTTGTGCAAGAAAA
ATTAAATGAAATAATAGAGTAAATAGAACAGAGGAAGAAAAGAAAAAAGTGGAAGCTGAAAAGCAA

Alignment

ORF - retro_lafr_813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.91 %
• Parental protein coverage: 54.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDYSEEQRNELEALESIYPDSFTVLSETPPSFTITVTSEAGENDETVQTTLKFTYSEKYPDDAPLYEIF
          MTDY..EQ.N.LE.LES...D.FT.LSE..P.F.ITVT.EAG.NDET.Q.TLKF.Y.EK.PD.APLYEIF
Retrocopy MTDYRDEQLNKLESLES---DFFTALSENSPRFAITVTPEAGKNDETAQITLKFRYNEKQPDEAPLYEIF

Parental  SQENLTDSDVSDILKLLALQAEENLGMVMIFTLVSAVQEKLNEIVDQI-KTRREEEKKQKEKE
          SQENL.D...S...K.LALQAE.NLG.V..FTLVS.VQEKLNEI...I..T..E..K...EK.
Retrocopy SQENLADNEISGDSKVLALQAEGNLGLVISFTLVSVVQEKLNEIIE*I<RTEEEKKKVEAEKQ

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_813 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005692	1 retrocopy	retro_amel_991,
Bos taurus	ENSBTAG00000009689	1 retrocopy	retro_btau_1004,
Callithrix jacchus	ENSCJAG00000004474	1 retrocopy	retro_cjac_1622,
Dasypus novemcinctus	ENSDNOG00000007516	1 retrocopy	retro_dnov_2467,
Equus caballus	ENSECAG00000006587	2 retrocopies	retro_ecab_216, retro_ecab_277,
Echinops telfairi	ENSETEG00000019085	3 retrocopies	retro_etel_140, retro_etel_1992, retro_etel_423,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813 ,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686,
Oryctolagus cuniculus	ENSOCUG00000013592	1 retrocopy	retro_ocun_691,
Procavia capensis	ENSPCAG00000005016	1 retrocopy	retro_pcap_114,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Ictidomys tridecemlineatus	ENSSTOG00000022124	1 retrocopy	retro_itri_596,
Tupaia belangeri	ENSTBEG00000002543	2 retrocopies	retro_tbel_2986, retro_tbel_4366,