RetrogeneDB ID: retro_lafr_1012

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:38716955..38717643(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPN
• Ensembl ID: ENSLAFG00000009458
• Aliases: None
• Description: Small nuclear ribonucleoprotein-associated protein [Source:UniProtKB/TrEMBL;Acc:G3T3S1]

Sequence

>retro_lafr_1012
CAGTGCATTGACTGTAGAGTGAGATGTATCCTGCAAGGTGGGTGAATCTGCATTGGTACCTTTAAGGCTTTTGATAGGCA
TATGAGCTCGACCCTCTGTGATTGTGATGAGTTCAGGAAGATCAAGCCAAAGAATGTGAAGCAGCCAGAATGTGAAGAAA
AGCGGGTTTTGGGTCTGGTGTTGCTGTGTGGGAAGAACATGGTTTCCATGACTTTTGTGGGAGTACCCCCACAAAGATAC
TGCTTTACCTGAGTTCCACTTGCTAGAGTTGCAGGAGGCCCTGGAGTTGGCAGGTCAGCTGGTAGAGGGGTACCAGCTGG
TGTCCCAGTTCCCCCGGCTCCTGGTCAATTAGCTGGGACTGTCAGAGGGGTTGGGGGGCCATCCCAAGAGGTAATATCGC
CCCAGGGAAGAGGCACCATAGCAGCTGCCTAGTTGCTGCTGCTGCTAGCATTACTGGAGCCCAAGCGCAGTACCCACCAG
GTAGGGAACCCCATCCCTACCTGTGGGCAGAGCAACCCTGTCTCCAGGCATTATGGCTCTTCCACCTGGTATAAGATCAG
CCATGGGGCTGCTGATTGGGCTCCCTTCTGCTCGAGGGACCCCAGTAGGCATGTCCCCTCCAGGAATGAGACCCCTTCTA
CCAGGAATTAGAGGTCTACCTTCCCCAGGAATGTGTCTGCCAAGACCC

Alignment

ORF - retro_lafr_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.41 %
• Parental protein coverage: 95.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNAKQPEREEKRVLGLVLLRGENLVSM
          Q.ID.R.RCILQ.G.I.IGTFKAFD.HM...LCDCDEFRKIKPKN.KQPE.EEKRVLGLVLL.G.N.VSM
Retrocopy QCIDCRVRCILQGG*ICIGTFKAFDRHMSSTLCDCDEFRKIKPKNVKQPECEEKRVLGLVLLCGKNMVSM

Parental  TVEGPPPKDTGIARVPLAGAAGGPGVGRAAGRGVPAGVPIPQAPAGLAGPVRGVGGPSQQVMTPQGRGTV
          T..G.PP.......VPLA..AGGPGVGR.AGRGVPAGVP.P.AP..LAG.VRGVGGPSQ.V..PQGRGT.
Retrocopy TFVGVPPQRYCFT*VPLARVAGGPGVGRSAGRGVPAGVPVPPAPGQLAGTVRGVGGPSQEVISPQGRGTI

Parental  AAA-AVAATASIAGAPTQYPPGR-GTPPPPVGRATPPPGIMAPPPGMRPPMGPPIGLPPTRGTPIGMPPP
          AAA..VAA.ASI.GA..QYPPGR.GTP..PVGRAT..PGIMA.PPG.R..MG..IGLP..RGTP.GM.PP
Retrocopy AAA<LVAAAASITGAQAQYPPGR<GTPSLPVGRATLSPGIMALPPGIRSAMGLLIGLPSARGTPVGMSPP

Parental  GMRPPPPGIRGPPPPGMRPPRP
          GMRP..PGIRG.P.PGM..PRP
Retrocopy GMRPLLPGIRGLPSPGMCLPRP

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_1012 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 21 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007034	3 retrocopies	retro_amel_1048, retro_amel_714, retro_amel_839,
Bos taurus	ENSBTAG00000008251	1 retrocopy	retro_btau_620,
Canis familiaris	ENSCAFG00000010127	6 retrocopies	retro_cfam_1753, retro_cfam_1874, retro_cfam_2039, retro_cfam_627, retro_cfam_682, retro_cfam_752,
Choloepus hoffmanni	ENSCHOG00000001846	2 retrocopies	retro_chof_2275, retro_chof_385,
Cavia porcellus	ENSCPOG00000020270	1 retrocopy	retro_cpor_878,
Felis catus	ENSFCAG00000022298	2 retrocopies	retro_fcat_1390, retro_fcat_1895,
Homo sapiens	ENSG00000128739	1 retrocopy	retro_hsap_2580,
Gorilla gorilla	ENSGGOG00000003988	1 retrocopy	retro_ggor_1615,
Loxodonta africana	ENSLAFG00000009458	1 retrocopy	retro_lafr_1012 ,
Myotis lucifugus	ENSMLUG00000023361	3 retrocopies	retro_mluc_1192, retro_mluc_1816, retro_mluc_2156,
Macaca mulatta	ENSMMUG00000023139	1 retrocopy	retro_mmul_644,
Mustela putorius furo	ENSMPUG00000014638	1 retrocopy	retro_mputfur_1080,
Mus musculus	ENSMUSG00000000948	3 retrocopies	retro_mmus_1285, retro_mmus_1733, retro_mmus_665,
Oryctolagus cuniculus	ENSOCUG00000003532	4 retrocopies	retro_ocun_1291, retro_ocun_488, retro_ocun_689, retro_ocun_846,
Otolemur garnettii	ENSOGAG00000007392	5 retrocopies	retro_ogar_1179, retro_ogar_3042, retro_ogar_3060, retro_ogar_475, retro_ogar_722,
Pongo abelii	ENSPPYG00000006269	1 retrocopy	retro_pabe_1900,
Pan troglodytes	ENSPTRG00000006826	1 retrocopy	retro_ptro_1507,
Rattus norvegicus	ENSRNOG00000015976	6 retrocopies	retro_rnor_1122, retro_rnor_1314, retro_rnor_1485, retro_rnor_2161, retro_rnor_2462, retro_rnor_2517,
Sus scrofa	ENSSSCG00000028124	2 retrocopies	retro_sscr_350, retro_sscr_405,
Ictidomys tridecemlineatus	ENSSTOG00000001339	1 retrocopy	retro_itri_44,
Tursiops truncatus	ENSTTRG00000010966	5 retrocopies	retro_ttru_1005, retro_ttru_1051, retro_ttru_1473, retro_ttru_580, retro_ttru_600,