RetrogeneDB ID: retro_lafr_1033

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:63210735..63211032(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028237
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSLAFG00000006412
• Aliases: None
• Description: None

Sequence

>retro_lafr_1033
ATGATGCCGTCTTGTACCAACCTGGCTATTGGGATCCCCAGTAGTAAAGTGAAATACCTGAGGCTCTGCAGCACAGACGA
TGGCTACACTGACCTTCAGTTTAAGAAAAGCCCTTCTAAGATCCCTTATAAGGCCGCTGCACTTGCCACTGTGCTGTTTT
TGATTGGTGTCTTTTTCACTACTATAGGCTCCCTCCTTCTGGTGGGTTACATCAGCAAAAGTGGGGAGCAGGCCAGGCCG
TTCCCCATCCTGATCACTGGCATCCTGGTGTTTCTACTAGAATTCCACCACTTGCAA

Alignment

ORF - retro_lafr_1033 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 81.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMSSRTNLATGIPSSKVKYSRLASTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIIIGSLLLAGY
          MM.S.TNLA.GIPSSKVKY.RL.STDDGY.DLQFKKSP.KIPYKA.ALATVLFLIG.F...IGSLLL.GY
Retrocopy MMPSCTNLAIGIPSSKVKYLRLCSTDDGYTDLQFKKSPSKIPYKAAALATVLFLIGVFFTTIGSLLLVGY

Parental  ISKGGAD-RAVPVLIIGILVFLPGFYHLR
          ISK.G...R..P.LI.GILVFL..F.HL.
Retrocopy ISKSGEQARPFPILITGILVFLLEFHHLQ

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_1033 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 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Choloepus hoffmanni	ENSCHOG00000010231	12 retrocopies	retro_chof_1228, retro_chof_1463, retro_chof_1812, retro_chof_2199, retro_chof_2210, retro_chof_2400, retro_chof_253, retro_chof_2584, retro_chof_2661, retro_chof_397, retro_chof_884, retro_chof_996,
Callithrix jacchus	ENSCJAG00000021275	2 retrocopies	retro_cjac_3112, retro_cjac_4206,
Erinaceus europaeus	ENSEEUG00000014992	1 retrocopy	retro_eeur_77,
Homo sapiens	ENSG00000089063	3 retrocopies	retro_hsap_4890, retro_hsap_550, retro_hsap_783,
Loxodonta africana	ENSLAFG00000006412	1 retrocopy	retro_lafr_1033 ,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Macaca mulatta	ENSMMUG00000013258	4 retrocopies	retro_mmul_1187, retro_mmul_2386, retro_mmul_2626, retro_mmul_856,
Nomascus leucogenys	ENSNLEG00000007719	3 retrocopies	retro_nleu_1256, retro_nleu_199, retro_nleu_723,
Otolemur garnettii	ENSOGAG00000001386	2 retrocopies	retro_ogar_1700, retro_ogar_3108,
Pongo abelii	ENSPPYG00000010796	3 retrocopies	retro_pabe_3801, retro_pabe_507, retro_pabe_916,
Pan troglodytes	ENSPTRG00000013221	4 retrocopies	retro_ptro_3030, retro_ptro_3257, retro_ptro_3258, retro_ptro_413,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35,