RetrogeneDB ID: retro_lafr_829

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:2636574..2637171(-)
• Located in intron of: ENSLAFG00000014451

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL13
• Ensembl ID: ENSLAFG00000004054
• Aliases: None
• Description: 60S ribosomal protein L13 [Source:UniProtKB/TrEMBL;Acc:G3STJ5]

Sequence

>retro_lafr_829
ATGGCACCCAGCCAGAATGGCATGGTTCTGACTCACCGCTTCCAGAAGGATGGGCAGCGGTGCATGGCCACAGGTTCAAC
CAGCCAGTGCAGAAGATCCACAGACAGAAGGCCCAACAAGGAAAAGCCCACAGCACCCTGCATCCTGATGTATCCACCCA
TAGTGCAGTACCACATGGTGAAGTATTAAACCAAAGTCTGAGCTGCCAGGAGGTTCAGCTTGAACGAGCTGAGGGTGGCT
GGCACCCACAAGCAGGTGGTCCAGACCATGAGTATCTCTATGGATCCACATAAGCGGAACAAGTCCACAGATTCCCTATG
GTCCAACGTGCAGCAGAGGAAGGAGTATCACTCCTAGCTCATTCTCTTCCCCCAGAAGCCATCAATCACGACAAGGGAGA
CAGCTCTACTCCGGAACTCAAACTGGCCACTCAGCTGACGGGACCAGAGATGTCCATACAGAACATCCGCTAGGAGGAGA
AATTCCGGGTCATCACCAGGAAGATAAGGACTTAATGGCCTTTGCCAGTCTTTTCTCGGCCCATGCCAGTGCTCAGCTCT
CAGCATCCACGGAAAGAGGGGCAAGGAATCCGCAGAG

Alignment

ORF - retro_lafr_829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVRCPTVRYHTKV
          MAPS.NGM.L...F.KD.QR..AT......R....R..R..K....AP.....P..PIV....V.Y.TKV
Retrocopy MAPSQNGMVLTHRFQKDGQRCMATGSTSQCRRSTDR--RPNKEKPTAPCILMYP--PIVQYHMVKY*TKV

Parental  RAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAP-KKGDS
          .A.R.FSL.ELRVAG.HK.V..T..IS.DP..RNKST.SL..NVQ..KEY.S.LILFP.KPS....KGDS
Retrocopy *AARRFSLNELRVAGTHKQVVQTMSISMDPHKRNKSTDSLWSNVQQRKEYHS*LILFPQKPSIT<DKGDS

Parental  SAEELKLATQLTGPVMPIRNVYKKEKARAIT-QEEKDFKAFASLRMARANARL-FGIRAKRAKEAAE
          S..ELKLATQLTGP.M.I.N....EK.R.IT.QE.KD..AFASL..A.A.A.L...I..KR.KE.AE
Retrocopy STPELKLATQLTGPEMSIQNIR*EEKFRVIT<QEDKDLMAFASLFSAHASAQL<LSIHGKRGKESAE

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_829 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 11 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017072	1 retrocopy	retro_acar_70,
Canis familiaris	ENSCAFG00000019840	5 retrocopies	retro_cfam_1135, retro_cfam_1919, retro_cfam_2122, retro_cfam_565, retro_cfam_897,
Callithrix jacchus	ENSCJAG00000009672	5 retrocopies	retro_cjac_2607, retro_cjac_2961, retro_cjac_4054, retro_cjac_663, retro_cjac_747,
Echinops telfairi	ENSETEG00000015057	4 retrocopies	retro_etel_1240, retro_etel_1382, retro_etel_1606, retro_etel_703,
Gorilla gorilla	ENSGGOG00000025427	6 retrocopies	retro_ggor_1548, retro_ggor_1963, retro_ggor_2231, retro_ggor_2732, retro_ggor_562, retro_ggor_767,
Loxodonta africana	ENSLAFG00000004054	5 retrocopies	retro_lafr_659, retro_lafr_766, retro_lafr_827, retro_lafr_828, retro_lafr_829 ,
Macaca mulatta	ENSMMUG00000017928	7 retrocopies	retro_mmul_2021, retro_mmul_2150, retro_mmul_2350, retro_mmul_579, retro_mmul_593, retro_mmul_737, retro_mmul_781,
Monodelphis domestica	ENSMODG00000003663	4 retrocopies	retro_mdom_1001, retro_mdom_416, retro_mdom_439, retro_mdom_674,
Mus musculus	ENSMUSG00000000740	23 retrocopies	retro_mmus_1091, retro_mmus_1522, retro_mmus_1533, retro_mmus_1854, retro_mmus_2074, retro_mmus_2163, retro_mmus_2186, retro_mmus_2321, retro_mmus_2333, retro_mmus_2351, retro_mmus_25, retro_mmus_2668, retro_mmus_2718, retro_mmus_3097, retro_mmus_3274, retro_mmus_3453, retro_mmus_3489, retro_mmus_3500, retro_mmus_355, retro_mmus_3711, retro_mmus_692, retro_mmus_732, retro_mmus_863,
Ornithorhynchus anatinus	ENSOANG00000006729	1 retrocopy	retro_oana_78,
Rattus norvegicus	ENSRNOG00000015335	14 retrocopies	retro_rnor_1054, retro_rnor_1260, retro_rnor_158, retro_rnor_160, retro_rnor_1719, retro_rnor_1720, retro_rnor_1834, retro_rnor_1848, retro_rnor_2471, retro_rnor_2574, retro_rnor_2608, retro_rnor_2787, retro_rnor_2854, retro_rnor_682,