RetrogeneDB ID: retro_lafr_683

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_3:83625068..83625617(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL6
• Ensembl ID: ENSLAFG00000002201
• Aliases: None
• Description: 60S ribosomal protein L6 [Source:UniProtKB/TrEMBL;Acc:G3SQ07]

Sequence

>retro_lafr_683
TCTGCAATGTGCTCAAGAATGGCCAGGGCTAGCTAGAGAAAGTGTTCCGCAGCCATATCCAGGATTGAAAAAACAAAAAA
AAGAAGATTCTTGCTACTGTCTCAAAGCTGGTTGTTGGTCACAAGAATGGTGATACCCAAGTGTTTAAACCTGGAAAATG
GCTAGGTATTACCCTACAGAAGATTTGCCTCAAAAGCTAATAAAACATGACAAAAAAAATCCCATTAGTTAACATGTGAG
AAAACTGAGAGACAACATCACTCCTAGATCATTCTGCTCATCTTCACTACAAGCAACAGAGGCAAGAAGGTGGTTTTCAG
GAAGCAGCTGAGCAGGGGCTTGTTATTTGAGACTATACACCTTGTTCTCAGTTACGTTTCTTTACGTAGAACACACCATA
AATTTTTCATTGCCACCTCCACCAAAATTGGTACGAAAATTCCAAAACATCTCGCTAATGCCTACTTCAAGAATAAGAAG
CTGTATAATAAGCTCAGACACCAAGAAGGTGACATCTTTGATACAGAGAAAAAGAAGTACATGCTTACC

Alignment

ORF - retro_lafr_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.58 %
• Parental protein coverage: 63.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SAMYSRKAMYK-RKYSAAKSRVEK-KKKEKVLATVTKPVGGDKNGGTRVVK-LRKMPRYYPTEDVPRKLL
          SAM.SR.A....RK.SAA.SR.EK..KK.K.LATV.K.V.G.KNG.T.V.K...KM.RYYPTED.P.KL.
Retrocopy SAMCSRMARAS*RKCSAAISRIEK<NKKKKILATVSKLVVGHKNGDTQVFK<TWKMARYYPTEDLPQKLI

Parental  SHGKK-PFSQHVRKLRSSITPGT-VLIILTGRHRGKRVIFLKQLDSGLLLVTGPLSLNRVPLRRTHQKFV
          .H.KK.P.S.HVRKLR..ITP....L.I.T...RGK.V.F.KQL..GLL..T..L.L..V.LRRTH.KF.
Retrocopy KHDKKNPIS*HVRKLRDNITPRS<ILLIFTTSNRGKKVVFRKQLSRGLLFETIHLVLSYVSLRRTHHKFF

Parental  IATSTKIDISGVKIPKHLTDTYFKKKKL-RKPRHQEGEIFDTEKEKYEIT
          IATSTKI...G.KIPKHL...YFK.KKL..K.RHQEG.IFDTEK.KY..T
Retrocopy IATSTKI---GTKIPKHLANAYFKNKKLYNKLRHQEGDIFDTEKKKYMLT

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_683 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.

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 123 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003060	1 retrocopy	retro_acar_171,
Bos taurus	ENSBTAG00000031723	6 retrocopies	retro_btau_1038, retro_btau_1117, retro_btau_1305, retro_btau_16, retro_btau_424, retro_btau_809,
Canis familiaris	ENSCAFG00000008873	1 retrocopy	retro_cfam_36,
Choloepus hoffmanni	ENSCHOG00000002917	13 retrocopies	retro_chof_1152, retro_chof_1285, retro_chof_1334, retro_chof_1688, retro_chof_2127, retro_chof_2151, retro_chof_2164, retro_chof_321, retro_chof_421, retro_chof_532, retro_chof_587, retro_chof_930, retro_chof_976,
Callithrix jacchus	ENSCJAG00000012450	7 retrocopies	retro_cjac_1362, retro_cjac_1620, retro_cjac_1949, retro_cjac_2723, retro_cjac_328, retro_cjac_349, retro_cjac_497,
Cavia porcellus	ENSCPOG00000013526	8 retrocopies	retro_cpor_1105, retro_cpor_1149, retro_cpor_1486, retro_cpor_382, retro_cpor_412, retro_cpor_651, retro_cpor_731, retro_cpor_982,
Dasypus novemcinctus	ENSDNOG00000017032	3 retrocopies	retro_dnov_1370, retro_dnov_1910, retro_dnov_2098,
Equus caballus	ENSECAG00000017514	1 retrocopy	retro_ecab_811,
Felis catus	ENSFCAG00000006858	12 retrocopies	retro_fcat_1264, retro_fcat_1370, retro_fcat_1844, retro_fcat_232, retro_fcat_398, retro_fcat_500, retro_fcat_625, retro_fcat_637, retro_fcat_643, retro_fcat_690, retro_fcat_926, retro_fcat_935,
Gorilla gorilla	ENSGGOG00000003372	16 retrocopies	retro_ggor_1602, retro_ggor_1893, retro_ggor_1898, retro_ggor_2047, retro_ggor_2138, retro_ggor_236, retro_ggor_2569, retro_ggor_2597, retro_ggor_2709, retro_ggor_2745, retro_ggor_290, retro_ggor_2938, retro_ggor_356, retro_ggor_426, retro_ggor_566, retro_ggor_816,
Loxodonta africana	ENSLAFG00000002201	2 retrocopies	retro_lafr_157, retro_lafr_683 ,
Macaca mulatta	ENSMMUG00000007433	1 retrocopy	retro_mmul_171,
Monodelphis domestica	ENSMODG00000003096	4 retrocopies	retro_mdom_1556, retro_mdom_1624, retro_mdom_1784, retro_mdom_615,
Mustela putorius furo	ENSMPUG00000002526	9 retrocopies	retro_mputfur_1116, retro_mputfur_1279, retro_mputfur_1320, retro_mputfur_1367, retro_mputfur_1407, retro_mputfur_1445, retro_mputfur_1489, retro_mputfur_401, retro_mputfur_571,
Mus musculus	ENSMUSG00000029614	13 retrocopies	retro_mmus_1264, retro_mmus_1336, retro_mmus_1898, retro_mmus_2684, retro_mmus_276, retro_mmus_3065, retro_mmus_3579, retro_mmus_3611, retro_mmus_3622, retro_mmus_3719, retro_mmus_445, retro_mmus_465, retro_mmus_730,
Nomascus leucogenys	ENSNLEG00000027093	2 retrocopies	retro_nleu_1813, retro_nleu_43,
Oryctolagus cuniculus	ENSOCUG00000003802	5 retrocopies	retro_ocun_129, retro_ocun_17, retro_ocun_189, retro_ocun_229, retro_ocun_245,
Pongo abelii	ENSPPYG00000025855	13 retrocopies	retro_pabe_1764, retro_pabe_1891, retro_pabe_2451, retro_pabe_2493, retro_pabe_2573, retro_pabe_2897, retro_pabe_3314, retro_pabe_358, retro_pabe_3677, retro_pabe_3725, retro_pabe_43, retro_pabe_472, retro_pabe_868,
Rattus norvegicus	ENSRNOG00000025936	1 retrocopy	retro_rnor_129,
Sarcophilus harrisii	ENSSHAG00000007096	2 retrocopies	retro_shar_506, retro_shar_536,
Ictidomys tridecemlineatus	ENSSTOG00000009409	3 retrocopies	retro_itri_1024, retro_itri_1125, retro_itri_684,