RetrogeneDB ID: retro_lafr_271

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_11:14015224..14015812(+)
• Located in intron of: ENSLAFG00000001353

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNAO1
• Ensembl ID: ENSLAFG00000002314
• Aliases: None
• Description: None

Sequence

>retro_lafr_271
CAGATCTTGCAGGAGTGATTATACAGTTTTGGCAAGATGGGGAAGCAAGCTTCCTTCAGTAGCTCCAAGGACTATCAACT
CAATAATTCTGGTTCATATTACCTAAATGATTTGGACAGACCATCCCCAACCAACTATATCCCAACTCAACAAGATGTCC
TTTGGACAAGAGTGAAGACCACAGGCATTGTGGAAATGCATTTCACCTTCGAAGACCTATACTTCAAGATGTTTGAAGTA
GATGGCCAAAGATAGGAATGAAAAAAAGTGGATTCACTGTTTTGGGAGAGTGACAGCAATTATCTTCTGTGTGGCCCTCA
ATGATTATGACCTTGCTGTGCCTGAGGTTGAAGAGATGAACTGAAGGCATGAAAGCATGAAACTGACAGCATTTGTAACA
ACAGATGGTTTACAGCCAGTTCAATTATTCTCTTCCTCAACAAGAAAGACCTTTTTGAGGAAAAACTGAGGAGTCCATTA
ACCATCTGTTATCCAGAATACACAGGTTCCAATAAATATGAAGAGGCAGTTGCTTACATTCACTGATAGTTTGAAGATTT
GAACAGAAGATACCAAAGAGATCTACAC

Alignment

ORF - retro_lafr_271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.0 %
• Parental protein coverage: 55.93 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELLSAMMRLWGDSGIQECFNRSREYQLNDSAKYYLDSLDRIGASDYQPTEQDILRTRVKTTGIVETHFTF
          ..L.......G..G.Q..F..S..YQLN.S..YYL..LDR.....Y.PT.QD.L.TRVKTTGIVE.HFTF
Retrocopy QILQE*LYSFGKMGKQASFSSSKDYQLNNSGSYYLNDLDRPSPTNYIPTQQDVLWTRVKTTGIVEMHFTF

Parental  KNLHFRLFDVGGQRSE-RKKWIHCFEDVTAIIFCVALSGYDQVLHEDETTNRMHESLMLFDSIC-NNKFF
          ..L.F..F.V.GQR.E..KKWIHCF..VTAIIFCVAL..YD....E.E..N..HES..L......N..F.
Retrocopy EDLYFKMFEVDGQR*E>EKKWIHCFGRVTAIIFCVALNDYDLAVPEVEEMN*RHESMKLTAFVT<NRWFT

Parental  IDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDAAAYIQAQFESKNRSPNKEIY
          ....I.....K.DLF.EK...SPLTIC.PEYTG.N.YE.A.AYI...FE..NR.......
Retrocopy ASSIILFLNKK-DLFEEKL-RSPLTICYPEYTGSNKYEEAVAYIH**FEDLNRRYQRDLH

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_271 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002314	1 retrocopy	retro_lafr_271 ,