RetrogeneDB ID: retro_lafr_912

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_49:14485818..14486540(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPIC
• Ensembl ID: ENSLAFG00000015661
• Aliases: None
• Description: None

Sequence

>retro_lafr_912
ACTTATATTGACGAAGACAAACTGGGTCAAGCATTTGAGGATGCTTTTCAGGTACAGAGGCAACATTCAACTGGCGATCC
TCCATACTCCCTAGACTTCAAAAATTACCTGGTTTTCATCAACCATTGCCTGCATGTCAGAGGAAGCTCCCATGACTATA
GAGGGTTGCCTACAGAGAAGCCTGTCTATACCTGGAGAACTGTAATCAACAGTGCTGCAGCTACTGTTTCGAAGGAAATA
TTCATCAATCTCTGCAGAGTATCACTGAAAACCAGCTAGTACCACCTGCTGTTCTCCAGCAAAAGGGAGGAAAAGGCAGG
AAGAAGCTCCCACTGTTTGAATACCTTTCATGAATCCCTCCGTAATCCCAAAAAGGCATCTTGTATTCAGTGGGTAGATA
TAACCAAAGGCATCTTTCAGTTTGTATCAGAAAAACACGGAAAGACACACAGAGCTTTGGGGAAAAAGAAAAGGCAACCG
GAAGACCCTGACTCACCAGAAAATAGCCAGAGCGCTGATGAATTATGGAAGAACTGGGAAAACCACCAAAAATCCAGAGA
AAGCTAGCTTACCAGTTCAGTGAGACCATTCTCCAGAGACTTTCTCCATGTTATTTCTTGGGGAAAGAGGTCTTCTACTC
ATAGTATGTCCAACGTGATCAAGAATATCTCAGCTTAAATAACTGGAACACAAGTTATAATCATACAGATGCCAATTACC
AT

Alignment

ORF - retro_lafr_912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.05 %
• Parental protein coverage: 99.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TCIEQDKLGQAFEDAFEVLRQHSAGDLQYSPDYKNYLAFINHCPHVRGNPNCYGMLPTEEPVYNWRTVIN
          T.I..DKLGQAFEDAF.V.RQHS.GD..YS.D.KNYL.FINHC.HVRG....Y..LPTE.PVY.WRTVIN
Retrocopy TYIDEDKLGQAFEDAFQVQRQHSTGDPPYSLDFKNYLVFINHCLHVRGSSHDYRGLPTEKPVYTWRTVIN

Parental  SAA-DYYFEGNIHQSLQNIAESQLVQPAVLQQKGGKGRKKLRLFEYL-HESLCNPEMASCIQWVDKTKGI
          SAA..Y.FEGNIHQSLQ.I.E.QLV.PAVLQQKGGKGRKKL.LFEYL.HESL.NP..ASCIQWVD.TKGI
Retrocopy SAA<SYCFEGNIHQSLQSITENQLVPPAVLQQKGGKGRKKLPLFEYL>HESLRNPKKASCIQWVDITKGI

Parental  FQFVS-KNKERLAELWGKRKGNRKTMTYQKMARALRNYGRTGEIT-KIRRKLTYQFSEAILQRLSPSYFL
          FQFVS.KN.ER..ELWGKRKGNRKT.T.QK.ARAL.NYGRTG..T.KI.RKL.YQFSE.ILQRLSP.YFL
Retrocopy FQFVS>KNTERHTELWGKRKGNRKTLTHQKIARALMNYGRTGKTT>KIQRKLAYQFSETILQRLSPCYFL

Parental  GKEIFYSQYIQPDQEYLSLNNWNASYNPMYANYH
          GKE.FYS.Y.Q.DQEYLSLNNWN.SYN...ANYH
Retrocopy GKEVFYS*YVQRDQEYLSLNNWNTSYNHTDANYH

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_912 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 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009904	2 retrocopies	retro_btau_1281, retro_btau_1837,
Callithrix jacchus	ENSCJAG00000001906	1 retrocopy	retro_cjac_3835,
Dasypus novemcinctus	ENSDNOG00000004496	1 retrocopy	retro_dnov_759,
Equus caballus	ENSECAG00000009614	1 retrocopy	retro_ecab_542,
Echinops telfairi	ENSETEG00000004217	6 retrocopies	retro_etel_1675, retro_etel_2007, retro_etel_2008, retro_etel_593, retro_etel_929, retro_etel_933,
Homo sapiens	ENSG00000166211	4 retrocopies	retro_hsap_1748, retro_hsap_1800, retro_hsap_3135, retro_hsap_864,
Gorilla gorilla	ENSGGOG00000024597	4 retrocopies	retro_ggor_1324, retro_ggor_1362, retro_ggor_2255, retro_ggor_703,
Loxodonta africana	ENSLAFG00000015661	1 retrocopy	retro_lafr_912 ,
Myotis lucifugus	ENSMLUG00000011052	1 retrocopy	retro_mluc_2169,
Macaca mulatta	ENSMMUG00000020873	1 retrocopy	retro_mmul_1245,
Nomascus leucogenys	ENSNLEG00000006232	1 retrocopy	retro_nleu_53,
Oryctolagus cuniculus	ENSOCUG00000008070	1 retrocopy	retro_ocun_161,
Otolemur garnettii	ENSOGAG00000015148	1 retrocopy	retro_ogar_1782,
Pongo abelii	ENSPPYG00000004873	4 retrocopies	retro_pabe_1444, retro_pabe_1445, retro_pabe_2819, retro_pabe_686,
Pan troglodytes	ENSPTRG00000005351	4 retrocopies	retro_ptro_1206, retro_ptro_1218, retro_ptro_3070, retro_ptro_598,
Rattus norvegicus	ENSRNOG00000005720	1 retrocopy	retro_rnor_1519,
Ictidomys tridecemlineatus	ENSSTOG00000015457	3 retrocopies	retro_itri_1785, retro_itri_235, retro_itri_29,
Tursiops truncatus	ENSTTRG00000017205	1 retrocopy	retro_ttru_1708,