RetrogeneDB ID: retro_lafr_639

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_27:22726751..22727420(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR82
• Ensembl ID: ENSLAFG00000028309
• Aliases: None
• Description: None

Sequence

>retro_lafr_639
AGACCAAAGAGAACCCTGTACAGTAAGAGATACGGTGTGGACCTCATCAGATACACACATGAGGCAAACACTGTCATTTA
CAGCTCTAAGAAAATAGATGATACTGTTTGTTACCTGACCTTGCGTGACAACAAATACATCAGATACTTTCCTGGACATA
ACAAAAGGGTGGCAGCCTTGACCATGTCACCTGGGGATGACATTTTCATTTCTGGGTCTCTCGATAAAACCATTAGACCC
TGGGACCTTTGGTCTCCTAACTGCTAGGGCCTCATGCATTTTCAGGGCAAGCCAGTTTGTTCTTTTGATCCAGAAGGGTT
AATTTTTGCCGGTGTTAATTCTGGAATGGTCAAACTTTACGATCTTCATTCTTTTGATGAGGGACTGTTTGCGACGTTTA
AGGTACAATACAATCAGACTTGTGAGTGGATAGGACTGACGTTCAGCAAGGATGGCAAACTCATCCTCACCCTCACCAAT
GGCAGCTTCATCCATCTCATTGATGCATTCAAGGGAGTGGTGATGCACGCATTTGAGGGTTATGCCAACAGCAAAACTCT
CATACTGGAGGCTTCATTTACTCCAGACTCCCAGTTTATCATGATTGGTTCAGAGGATGGCAAGATCCACGTCTGGAATG
GAGAGAGCGGCATCAAAGTAGCTGTGCTG

Alignment

ORF - retro_lafr_639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.89 %
• Parental protein coverage: 70.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPKRTLYSKKYGVDLIRYTHAANTVVYSSNKIDDTIRYLSLHDNKYIRYFPGHSKRVVALSMSPVDDTFI
          .PKRTLYSK.YGVDLIRYTH.ANTV.YSS.KIDDT..YL.L.DNKYIRYFPGH.KRV.AL.MSP.DD.FI
Retrocopy RPKRTLYSKRYGVDLIRYTHEANTVIYSSKKIDDTVCYLTLRDNKYIRYFPGHNKRVAALTMSPGDDIFI

Parental  SGSLDKTIRLWDLRSPNCQGLMHLQGKPVCSFDPEGLIFAAGVNSEMVKLYDLRSFDKGPFATFKMQYDR
          SGSLDKTIR.WDL.SPNC.GLMH.QGKPVCSFDPEGLIFA.GVNS.MVKLYDL.SFD.G.FATFK.QY..
Retrocopy SGSLDKTIRPWDLWSPNC*GLMHFQGKPVCSFDPEGLIFA-GVNSGMVKLYDLHSFDEGLFATFKVQYNQ

Parental  TCEWTGLKFSNDGKLILISTNGSFIRLIDAFKGVVMHTFGGYANSKAVTLEASFTPDSQFIMI---DSYV
          TCEW.GL.FS.DGKLIL..TNGSFI.LIDAFKGVVMH.F.GYANSK...LEASFTPDSQFIMI...D...
Retrocopy TCEWIGLTFSKDGKLILTLTNGSFIHLIDAFKGVVMHAFEGYANSKTLILEASFTPDSQFIMIGSEDGKI

Parental  SHYTKRNGINIVLL
          .......GI....L
Retrocopy HVWNGESGIKVAVL

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_639 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000774	1 retrocopy	retro_chof_2299,
Callithrix jacchus	ENSCJAG00000006114	1 retrocopy	retro_cjac_3022,
Homo sapiens	ENSG00000164091	2 retrocopies	retro_hsap_2816, retro_hsap_419,
Loxodonta africana	ENSLAFG00000028309	1 retrocopy	retro_lafr_639 ,
Macropus eugenii	ENSMEUG00000009280	1 retrocopy	retro_meug_1207,
Macaca mulatta	ENSMMUG00000008234	2 retrocopies	retro_mmul_339, retro_mmul_511,
Monodelphis domestica	ENSMODG00000011614	4 retrocopies	retro_mdom_1259, retro_mdom_144, retro_mdom_219, retro_mdom_398,
Nomascus leucogenys	ENSNLEG00000007104	2 retrocopies	retro_nleu_1016, retro_nleu_1195,
Otolemur garnettii	ENSOGAG00000016032	1 retrocopy	retro_ogar_1314,
Pongo abelii	ENSPPYG00000013812	2 retrocopies	retro_pabe_185, retro_pabe_300,
Rattus norvegicus	ENSRNOG00000048441	3 retrocopies	retro_rnor_1003, retro_rnor_1109, retro_rnor_1152,