RetrogeneDB ID: retro_lafr_1188

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_85:3239662..3240267(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000020970
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBMX
• Ensembl ID: ENSLAFG00000005568
• Aliases: None
• Description: None

Sequence

>retro_lafr_1188
GAAGCCAACTGTCCAGGAAAGCTCTCCATTGGTGGGCTCAATACAGAAACAAATACGAAAGCCCTTAAGGCAGTTTTTGG
CAAATATGGACGAAATGTGGAAGTACTCTTGATAAAAGACCGTGAAACCAACAAATCGAGAGGATTGCCTTTTGTCACCT
TTGAAAGCCCGGCAGATGCCAAAGATACAGCCAAAGATAGGAATGGAAAATCCTTAAATGGAAAAGCCATTAAAGTTGAA
CAAACCATTAACGTATCATTTGAAAGTGGTAGACGTGGACCTCCTCCAACCTCCAAGAAGCAGAGGCCCTTCAAGAGGTC
TTAGAGGAGGAAGTATAGGAACCAGGGAACCTCCTTCATATGGGGGGGTGGATAACAGATGATGGTACATATTCCATGAA
TTTTAACATGAGTTCTTTCAAGAGACCTCTTCCAATAAAAAGAGTACCACCACCACGAAATAGAGGTTCTCCTCCTAAAA
GATCTGCCCCTTTGGGACCAGTTCACGGCAGCAGTGGAATAGGAGGAAGAGCTCCTGTATCACATGGAAGGGATAGTTAT
GGAGGCCCACCACAAAGGGTACCCCTGCCCTCTCGTAGACATGTT

Alignment

ORF - retro_lafr_1188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.39 %
• Parental protein coverage: 51.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMNGK
          EA..PGKL.IGGLNTETN.KAL.AVFGKYGR.VEVLL.KDRETNKSRG..FVTFESPADAKD.A.D....
Retrocopy EANCPGKLSIGGLNTETNTKALKAVFGKYGRNVEVLLIKDRETNKSRGLPFVTFESPADAKDTAKDRXXX

Parental  SLDGKAIKVEQATKPTFESGRRGPPP-PPRSRGPPRGLRGGRGGSGGTRGPPS-RGGHMDDGG-YSMNFN
          ................FESGRRGPPP.PPRSRGP.RGLRGG...S.GTR.PPS..GG...D.G.YSMNFN
Retrocopy XXXXXXXXXXXXXXVSFESGRRGPPP>PPRSRGPSRGLRGG---SIGTREPPS>MGGWITDDGTYSMNFN

Parental  MSSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDV
          MSS...PLP.KR.PPPR..G.PPKRSAP.GPV..SSG.GGRAPVS.GRDSYGGPP.R.PLPSRR.V
Retrocopy MSSFKRPLPIKRVPPPRNRGSPPKRSAPLGPVHGSSGIGGRAPVSHGRDSYGGPPQRVPLPSRRHV

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_1188 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 27 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Dasypus novemcinctus	ENSDNOG00000017199	3 retrocopies	retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188 , retro_lafr_276, retro_lafr_35,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Monodelphis domestica	ENSMODG00000014054	1 retrocopy	retro_mdom_1231,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Otolemur garnettii	ENSOGAG00000007839	5 retrocopies	retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tarsius syrichta	ENSTSYG00000009555	1 retrocopy	retro_tsyr_15,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,