RetrogeneDB ID: retro_lafr_847

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:84144708..84145197(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH12
• Ensembl ID: ENSLAFG00000022637
• Aliases: None
• Description: None

Sequence

>retro_lafr_847
ATCAATAATGCAGGAGTGAAGATGTGTCCGTATTTCAAGACAGCTGATGACTTTGAGACTCCCCTGTGAGTCAACCACCT
GGGCCACTTTTTTCTCACCCATCTGCCCCTGCAGGGGCTAAAAGGGTCTGCTCCTGTATAGGTGGTGAACCTATCATCAG
TGGTCCACCATGCTGGCAAGCTTCACTTCCGTGACCTCCAGAATGAGAAGTGCTACAGCCAGGTTTTGCCTGTTGCCACA
GCAAACTGGAAAATGTGCTTTTTTTCTCAAGAACTGTCCAAGAAGCTCCAAGGCACTGGGGTCCCCATTTACGCAGTGCA
CCCGGACATCTTTCGCTCCCAGCTATTCTAGCACTCCTTCCTCCTGTGCCTGCTCTGGAGGCTCTTCTTCCCATTAATCA
AGTCAGTGCAGAAATGGGTGTAGACTAGCCTGCACTGTGCCCTGGCTGAGGGTCTGGAACCCCTGAGTGCCAAGTACTTC
AATGACTGC

Alignment

ORF - retro_lafr_847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.94 %
• Parental protein coverage: 51.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  INNAGVMMCPYSKTADGFETHLGVNHLGHFLLTHLLLERLKESAPSRVVNLSSVVHHVGKIHFHDLQGEK
          INNAGV.MCPY.KTAD.FET.L.VNHLGHF.LTHL.L..LK.SAP..VVNLSSVVHH.GK.HF.DLQ.EK
Retrocopy INNAGVKMCPYFKTADDFETPL*VNHLGHFFLTHLPLQGLKGSAPV*VVNLSSVVHHAGKLHFRDLQNEK

Parental  RYSR-GFAYCHSKLANVLF-TRELAKKLQGTGVTTYAVHPGIVHSELFRHSFLLCLLWRLFSPFVKSARE
          .YS..GFA.CHSKL.NVLF...EL.KKLQGTGV..YAVHP.I..S.LF.HSFLLCLLWRLF.P..KS...
Retrocopy CYSQ<GFACCHSKLENVLF>SQELSKKLQGTGVPIYAVHPDIFRSQLF*HSFLLCLLWRLFFPLIKSVQK

Parental  GAQTSLHCALAEGLEPLSGKYFSDC
          ...TSLHCALAEGLEPLS.KYF.DC
Retrocopy WV*TSLHCALAEGLEPLSAKYFNDC

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_847 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008036	1 retrocopy	retro_amel_673,
Canis familiaris	ENSCAFG00000016446	1 retrocopy	retro_cfam_2068,
Equus caballus	ENSECAG00000015001	1 retrocopy	retro_ecab_1059,
Felis catus	ENSFCAG00000014092	1 retrocopy	retro_fcat_1910,
Loxodonta africana	ENSLAFG00000022637	1 retrocopy	retro_lafr_847 ,
Macropus eugenii	ENSMEUG00000001473	1 retrocopy	retro_meug_41,
Meleagris gallopavo	ENSMGAG00000011960	1 retrocopy	retro_mgal_16,
Microcebus murinus	ENSMICG00000010855	1 retrocopy	retro_mmur_432,
Ornithorhynchus anatinus	ENSOANG00000015759	1 retrocopy	retro_oana_89,
Procavia capensis	ENSPCAG00000009359	1 retrocopy	retro_pcap_1,
Pelodiscus sinensis	ENSPSIG00000010721	1 retrocopy	retro_psin_24,
Sarcophilus harrisii	ENSSHAG00000012445	1 retrocopy	retro_shar_41,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,