RetrogeneDB ID: retro_lafr_686

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_30:12152848..12153298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPD
• Ensembl ID: ENSLAFG00000016483
• Aliases: None
• Description: None

Sequence

>retro_lafr_686
GGTGGTGTCGATGAGGTAGAATCCATAGAGCTCCTCACAGACAGCAAGACCAATAAGAGGCATGGATTCTGCTTTATTAT
CTTTAAGAGAGAGGAACAAGTGAAGAAAATAATGGAAAAGACATAGCACAATGTTGGTCCTAGTAAATGTAAAATAGAAG
TAGCCATGTCCCAAGAACAGTACCAGCAACAGGTACAGTGGGGATCTAGAGGAAGATTTGCAGGGAGAGCTCATGGAAGA
GGTGGTGGCTCCAGTCAAAACTGGAACCAGGGATATAGTAATTACTGGAACCAAGGCTATGGCAACTGTGGAGACAACAG
TCAAGTTTCCGGTGGTTACAGAGATCATGATTATACTGCTAACTACAACCACTATGGATGTGGTGATTATAGCAACCAGC
AGAGTGGCTGTGGGAAAGTATCCAGGTGAGGTAGTCATCAAAATAGCTAC

Alignment

ORF - retro_lafr_686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.33 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQYQQQQQWGSR
          GG..EVESIEL..D.KTNKR.GFCFI.FK.EE.VKKIMEK..HNVG.SKC.I.VAMS.EQYQQQ.QWGSR
Retrocopy GGVDEVESIELLTDSKTNKRHGFCFIIFKREEQVKKIMEKT*HNVGPSKCKIEVAMSQEQYQQQVQWGSR

Parental  GGFAGRARGRGGGPSQNWNQGYSNYWNQGYGNYGYNSQGYGGYGGYDYTGYNNYYGYGDYSNQQSGYGKV
          G.FAGRA.GRGGG.SQNWNQGYSNYWNQGYGN.G.NSQ..GGY...DYT...N.YG.GDYSNQQSG.GKV
Retrocopy GRFAGRAHGRGGGSSQNWNQGYSNYWNQGYGNCGDNSQVSGGYRDHDYTANYNHYGCGDYSNQQSGCGKV

Parental  SRRGGHQNSY
          SR.G.HQNSY
Retrocopy SR*GSHQNSY

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_686 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649,
Homo sapiens	ENSG00000138668	1 retrocopy	retro_hsap_4689,
Gorilla gorilla	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916,
Loxodonta africana	ENSLAFG00000001189	1 retrocopy	retro_lafr_405,
Loxodonta africana	ENSLAFG00000008612	1 retrocopy	retro_lafr_650,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686 ,
Loxodonta africana	ENSLAFG00000029587	5 retrocopies	retro_lafr_1202, retro_lafr_1208, retro_lafr_192, retro_lafr_747, retro_lafr_961,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752,
Tarsius syrichta	ENSTSYG00000010395	3 retrocopies	retro_tsyr_1092, retro_tsyr_2070, retro_tsyr_269,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Vicugna pacos	ENSVPAG00000004374	2 retrocopies	retro_vpac_484, retro_vpac_97,