RetrogeneDB ID: retro_lafr_928

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:63214067..63214442(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS8
• Ensembl ID: ENSLAFG00000008617
• Aliases: None
• Description: None

Sequence

>retro_lafr_928
CCAGTAATGGTGATGTGCAAAAAATGCCTTTAAAAAAAAAAATTGATGGCGGCCTAAGAACCAGGAATTCAAGGAACCTG
GTGGACTTGTTTTCCCCCCATACATGGTCAGCTCCTGGGCTTACAACTGCTCCAGAATTAAATGAAAAAATGCAAGATAA
CTTTGGAAAGAATACCATCTAGTACTAGGTTGGCAAATTCTGAACTTGGAATTTGTTCCGTAGGACAAAGAATCAGGCAA
ATTAATTTTGCTGGAATTAATGCAACCATTTGGAACCACCTGTAGTCTGAGATGATGCAGCCAAACAATACAACATATAG
AGATGCACAAAGGAGAGAGGTCTTTCCCCTGTTTTCTCAAGCAGGTACTTCAGTA

Alignment

ORF - retro_lafr_928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.67 %
• Parental protein coverage: 60.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PVAVM-AESAFSFKKLLDQCENQELEAPGGIATAP-VYGQLLALYLLYNDMN-NARYLWK-RIPPAIKSA
          PV.VM.A..AF..KK......NQE...PGG....P...GQLL.L.LL.N.M..NAR.LWK.RIP.....A
Retrocopy PVMVM>AKNAFK-KKN*WRPKNQEFKEPGGLVFPP<IHGQLLGLQLLQN*MK>NAR*LWK<RIPSSTRLA

Parental  NSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMAALRDATRGRAFALVSQAYTSI
          NSELG.I.SVGQRI.Q..F.GI..TI..H..SE..QP.....RDA.R...F.L.SQA.TS.
Retrocopy NSELG-ICSVGQRIRQINFAGINATIWNHL*SEMMQPNNTTYRDAQRREVFPLFSQAGTSV

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_928 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005854	3 retrocopies	retro_btau_1315, retro_btau_1401, retro_btau_1402,
Canis familiaris	ENSCAFG00000030168	1 retrocopy	retro_cfam_1327,
Dasypus novemcinctus	ENSDNOG00000015309	5 retrocopies	retro_dnov_1157, retro_dnov_1306, retro_dnov_149, retro_dnov_1701, retro_dnov_527,
Felis catus	ENSFCAG00000013789	1 retrocopy	retro_fcat_1648,
Loxodonta africana	ENSLAFG00000008617	1 retrocopy	retro_lafr_928 ,
Macropus eugenii	ENSMEUG00000008189	3 retrocopies	retro_meug_583, retro_meug_609, retro_meug_701,
Monodelphis domestica	ENSMODG00000007474	1 retrocopy	retro_mdom_1295,
Mustela putorius furo	ENSMPUG00000000068	1 retrocopy	retro_mputfur_176,
Mus musculus	ENSMUSG00000034432	1 retrocopy	retro_mmus_1812,
Oryctolagus cuniculus	ENSOCUG00000007341	4 retrocopies	retro_ocun_1549, retro_ocun_1579, retro_ocun_428, retro_ocun_550,
Pongo abelii	ENSPPYG00000013308	1 retrocopy	retro_pabe_3787,
Rattus norvegicus	ENSRNOG00000019635	3 retrocopies	retro_rnor_1005, retro_rnor_1078, retro_rnor_975,
Tupaia belangeri	ENSTBEG00000015944	1 retrocopy	retro_tbel_4315,