RetrogeneDB ID: retro_lafr_60

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_85:5588304..5588826(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000009657
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000013881
• Aliases: None
• Description: None

Sequence

>retro_lafr_60
ATGGCAGCAGTAATTCTAGGGGGAGACACCATGGGCCCAGAGGGTATCTTCCCCAATCAGACTGAGGAACTGGGGCCTCA
GGTAGGCCCCACAGAAGGCACTGGAGATTGGGGCAGTGAGGAACACAAGAAACACCAGGGGGAAGCATGGGCAGGTCCAA
CTGGTTACTCCTACCAGCCCCTGAACCAAGATTCTGAACAAGAGGAAGTGGAGTTGGCACTGGTGGGGGATGGAGATGTA
GTTGCTGACATCCAGGAGTGGTTCCAGTTCCTGGGGCTACATTTGCCAGACTCTCCATTAAAGAGTGAAGATGAAGAAGT
GGAGGGAGCTTCAGCATTGAAGAACTACAGCTATATTCCCATGGACCCAGAACACGTAGAGCTGATGAAAAGGACAATGG
ATGGAATAAGCCTGCCTGCACGAGCAGTTCCGGCCTGGGCTCTGGAGATCTCAGATGCTGAATGGGAAGATGTGATACAG
GAGGCCCTCCAAGCCCAGAAGGCATCACCAGCCTGGAAGTGA

Alignment

ORF - retro_lafr_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAVVLRGDTMGPERIFPNQTEELGPHVGPTEGTGDWSSEEHEEEQEEAGAGPAGYSYQPLNQDPEQEEV
          MAAV.L.GDTMGPE.IFPNQTEELGP.VGPTEGTGDW.SEEH...Q.EA.AGP.GYSYQPLNQD.EQEEV
Retrocopy MAAVILGGDTMGPEGIFPNQTEELGPQVGPTEGTGDWGSEEHKKHQGEAWAGPTGYSYQPLNQDSEQEEV

Parental  ELAPGGDGDVVADIQERIQAMGLHLPDPPLESEEEEEEGATALSNHSSIPMDPEHIELVKRTMAAVTLPA
          ELA..GDGDVVADIQE..Q..GLHLPD.PL.SE.EE.EGA.AL.N.S.IPMDPEH.EL.KRTM....LPA
Retrocopy ELALVGDGDVVADIQEWFQFLGLHLPDSPLKSEDEEVEGASALKNYSYIPMDPEHVELMKRTMDGISLPA

Parental  PGVPAWAQEISDAQWEDVVQKALQARQASPAWK
          ..VPAWA.EISDA.WEDV.Q.ALQA..ASPAWK
Retrocopy RAVPAWALEISDAEWEDVIQEALQAQKASPAWK

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_60 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012655	1 retrocopy	retro_amel_1620,
Bos taurus	ENSBTAG00000005536	1 retrocopy	retro_btau_240,
Canis familiaris	ENSCAFG00000001756	1 retrocopy	retro_cfam_1643,
Callithrix jacchus	ENSCJAG00000004894	2 retrocopies	retro_cjac_2054, retro_cjac_824,
Cavia porcellus	ENSCPOG00000022111	1 retrocopy	retro_cpor_1530,
Echinops telfairi	ENSETEG00000002439	1 retrocopy	retro_etel_236,
Felis catus	ENSFCAG00000031337	1 retrocopy	retro_fcat_1772,
Loxodonta africana	ENSLAFG00000013881	1 retrocopy	retro_lafr_60 ,
Myotis lucifugus	ENSMLUG00000012138	2 retrocopies	retro_mluc_1819, retro_mluc_851,
Monodelphis domestica	ENSMODG00000019002	1 retrocopy	retro_mdom_878,
Oryctolagus cuniculus	ENSOCUG00000001565	2 retrocopies	retro_ocun_1312, retro_ocun_1446,
Pelodiscus sinensis	ENSPSIG00000002330	1 retrocopy	retro_psin_56,
Pteropus vampyrus	ENSPVAG00000008711	1 retrocopy	retro_pvam_266,
Rattus norvegicus	ENSRNOG00000017144	2 retrocopies	retro_rnor_716, retro_rnor_961,
Tupaia belangeri	ENSTBEG00000012294	2 retrocopies	retro_tbel_1462, retro_tbel_3528,
Tursiops truncatus	ENSTTRG00000006996	1 retrocopy	retro_ttru_357,