RetrogeneDB ID: retro_lafr_1007

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:17970475..17971244(+)
• Located in intron of: ENSLAFG00000005888

Retrocopy information

• Ensembl ID: ENSLAFG00000028215
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS4X
• Ensembl ID: ENSLAFG00000002654
• Aliases: None
• Description: ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]

Sequence

>retro_lafr_1007
GGTCCCTAGAAGTGTCTAAAGAACGTAGCAGCTCCAAAGTGTTGGAGGCTGGACAAACTGACAGGCGTGTTTGCTCCTCA
TCCATCCACCGGTCCCCATAAGCTGAGAGAATGTCTCGCCCTCATTCTTTTCTTAAGGAACAGCCTCAAGTATGCCCTGA
AGAGAAGATGAAGTGAAGATCTACATGCAGCGGTTCACTAAGATTGATGATGGCAAGGTCCAAGCTGATGCAGCGTACCC
TGCAGGTTTTCTGATGTCATCGGCATCAACCAGATGGGAGAGAATTTCCACCTGACCTGTGACACCAAGGTTCGCTTTGC
TGTTTATCGTATTATGCCACAGTAGATGAACTACAGCTTGTGCAAATAAGAAAGATTTTGGGGGGCACAGAAGGAATACC
TCATCTGGTAAACCACATTGCTTGCACCATCTACATCCCTGATCCTCTCATCAAGGTGAATGACACCATTCAGATTAATT
TGGAGACCAGAAAGATGACCAGTTTCATCCGGTTCAACATGTGTACGGTGACTGGAGGTGTTAACCTGGAAGAATTGATG
TGAGCACTAACAGAGAGAGACGTCCCAGGTCTTTTGATGTGGTTCATGTGAAAGATGCCGGTGGCAACAGCTTTGTCACC
TGGCTTTCCAGCATTTTCATTATTGGCAAAGGCAACAAACCATAAATTTCTCTCCCCCTGAAGCAAAGTATCCACGTCAC
CACCGCTGAAAAAAGAGACAACTGTCTGGCTGCCAAACAGAGCAATGGG

Alignment

ORF - retro_lafr_1007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.81 %
• Parental protein coverage: 99.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTG-DEVKKICMQRFIKI
          GP.K.LK.VAAPK.W.LDKLTGVFAP.PSTGPHKLRECL.LI.FLRN.LKYAL...DEVK.I.MQRF.KI
Retrocopy GP*KCLKNVAAPKCWRLDKLTGVFAPHPSTGPHKLRECLALILFLRNSLKYALKR>DEVK-IYMQRFTKI

Parental  D-GKVRTDITYPAGFM-DVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCK-VRKIFVGTKGIPHL
          D.GKV..D..YPAGF..DVI.I...GENF.L..DTK.RFAV.RI.P....Y.LCK..RKI..GT.GIPHL
Retrocopy DDGKVQADAAYPAGFL<DVIGINQMGENFHLTCDTKVRFAVYRIMPQ*MNYSLCK<IRKILGGTEGIPHL

Parental  VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANL-GRIGVITNRERHPGSFDVV
          V.H.A.TI..PDPLIKVNDTIQI.LET.K.T.FI.F...N.C.VTGG.NL.GRI.V.TNRER.P.SFDVV
Retrocopy VNHIACTIYIPDPLIKVNDTIQINLETRKMTSFIRF---NMCTVTGGVNL<GRIDVSTNRERRPRSFDVV

Parental  HVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQSSG
          HVKDA.GNSF.T.LS.IF.IGKGNKP.ISLP....I..T.AE.RD..LAAKQS.G
Retrocopy HVKDAGGNSFVTWLSSIFIIGKGNKP*ISLPLKQSIHVTTAEKRDNCLAAKQSNG

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_1007 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 24 parental genes, and 166 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Ailuropoda melanoleuca	ENSAMEG00000005805	14 retrocopies	retro_amel_1003, retro_amel_1128, retro_amel_1296, retro_amel_1381, retro_amel_1695, retro_amel_1869, retro_amel_195, retro_amel_259, retro_amel_327, retro_amel_576, retro_amel_767, retro_amel_869, retro_amel_968, retro_amel_971,
Bos taurus	ENSBTAG00000018800	5 retrocopies	retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris	ENSCAFG00000017151	2 retrocopies	retro_cfam_165, retro_cfam_194,
Callithrix jacchus	ENSCJAG00000004192	2 retrocopies	retro_cjac_19, retro_cjac_361,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Felis catus	ENSFCAG00000012041	11 retrocopies	retro_fcat_1155, retro_fcat_1498, retro_fcat_1562, retro_fcat_1751, retro_fcat_1773, retro_fcat_2024, retro_fcat_229, retro_fcat_290, retro_fcat_454, retro_fcat_563, retro_fcat_766,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Gorilla gorilla	ENSGGOG00000023079	18 retrocopies	retro_ggor_1278, retro_ggor_1319, retro_ggor_1354, retro_ggor_1367, retro_ggor_1478, retro_ggor_1479, retro_ggor_1517, retro_ggor_1520, retro_ggor_1689, retro_ggor_223, retro_ggor_2676, retro_ggor_2719, retro_ggor_572, retro_ggor_711, retro_ggor_844, retro_ggor_894, retro_ggor_895, retro_ggor_939,
Loxodonta africana	ENSLAFG00000002654	4 retrocopies	retro_lafr_1007 , retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Macropus eugenii	ENSMEUG00000007969	16 retrocopies	retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Myotis lucifugus	ENSMLUG00000011685	5 retrocopies	retro_mluc_1638, retro_mluc_2253, retro_mluc_301, retro_mluc_536, retro_mluc_736,
Macaca mulatta	ENSMMUG00000003295	7 retrocopies	retro_mmul_1243, retro_mmul_1589, retro_mmul_1895, retro_mmul_1999, retro_mmul_2338, retro_mmul_43, retro_mmul_97,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus	ENSMUSG00000031320	13 retrocopies	retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Pongo abelii	ENSPPYG00000020462	24 retrocopies	retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586, retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325, retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes	ENSPTRG00000022025	9 retrocopies	retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Ictidomys tridecemlineatus	ENSSTOG00000028692	8 retrocopies	retro_itri_1179, retro_itri_1607, retro_itri_291, retro_itri_306, retro_itri_368, retro_itri_495, retro_itri_738, retro_itri_985,