RetrogeneDB ID: retro_lafr_550

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_21:295296..295633(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPMS2
• Ensembl ID: ENSLAFG00000018725
• Aliases: None
• Description: None

Sequence

>retro_lafr_550
ATTAAGTTTATATTAAGACAGCCAGTTGGTTTTGTTACCTTTGACAGCTGAGGCAGAAGTAGAAGTGGCCAAATATATAT
TCAGTGGCATTTGCTTCCATTCCTCAAACCAATAGACTCTGAGCTTAGAGTTTCCAAAGCCAATATCAAAATGACCACGA
ACAGACTGATGGTGACTTCAAATTCCACCAAGTCCACCCTAAACTGGGAGCACATTTCATTGAGGATTCCCATGACCTAG
TGGGAGAAGCACTTATCTTCATGTGCCTAGAAGTGTGGTTCTGTACATGGTGTACCCCACAAAACTGATTCTAAATATCA
CCCATGATGGATTCACT

Alignment

ORF - retro_lafr_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.85 %
• Parental protein coverage: 63.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IKLTSRQPVGFVIFDS-RAGAEAAKNALNGIRFDPENPQTLRLEF-AKANTKMAKSKLMATPNPTSA-HP
          IK...RQPVGFV.FDS..A..E.AK....GI.F...N..TL.LEF..KAN.KM....LM.T.N.T...HP
Retrocopy IKFILRQPVGFVTFDS>EAEVEVAKYIFSGICFHSSNQ*TLSLEF<SKANIKMTTNRLMVTSNSTKS<HP

Parental  ALGAHFIARDPYDLMGAALIPASPEAW-APYPLYTTELTPAISHAAFT
          .LGAHFI..D..DL.G.ALI....E.W...Y..Y.T.L...I.H..FT
Retrocopy KLGAHFI-EDSHDLVGEALIFMCLEVW<VLYMVYPTKLILNITHDGFT

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_550 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 17 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011037	1 retrocopy	retro_btau_1674,
Callithrix jacchus	ENSCJAG00000005200	2 retrocopies	retro_cjac_1775, retro_cjac_298,
Dipodomys ordii	ENSDORG00000004025	1 retrocopy	retro_dord_438,
Homo sapiens	ENSG00000166831	2 retrocopies	retro_hsap_2513, retro_hsap_3613,
Gorilla gorilla	ENSGGOG00000008984	1 retrocopy	retro_ggor_2438,
Loxodonta africana	ENSLAFG00000018725	6 retrocopies	retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550 , retro_lafr_859,
Macaca mulatta	ENSMMUG00000013270	1 retrocopy	retro_mmul_1837,
Monodelphis domestica	ENSMODG00000010487	1 retrocopy	retro_mdom_571,
Mus musculus	ENSMUSG00000032387	9 retrocopies	retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562, retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys	ENSNLEG00000012505	1 retrocopy	retro_nleu_2209,
Otolemur garnettii	ENSOGAG00000026017	1 retrocopy	retro_ogar_3254,
Pongo abelii	ENSPPYG00000006553	1 retrocopy	retro_pabe_2963,
Pan troglodytes	ENSPTRG00000007165	2 retrocopies	retro_ptro_1458, retro_ptro_2441,
Sus scrofa	ENSSSCG00000004549	1 retrocopy	retro_sscr_851,
Ictidomys tridecemlineatus	ENSSTOG00000010055	2 retrocopies	retro_itri_1512, retro_itri_556,
Tarsius syrichta	ENSTSYG00000008996	3 retrocopies	retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus	ENSTTRG00000011840	3 retrocopies	retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,