RetrogeneDB ID: retro_lafr_784

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_38:4739485..4739856(-)
• Located in intron of: ENSLAFG00000002605

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11ORF67
• Ensembl ID: ENSLAFG00000000518
• Aliases: None
• Description: None

Sequence

>retro_lafr_784
ATGTGTTCTCCTGAAATGGCTTTCCTCTCCTGGGAACAAATTAAAGTACAAGGTTCTACTAAAACCTGTAAGGACTGTAA
AGTGTGGCCAGGGTCAGTCCAGTTTGGAATCAGAGAGAAACAAGAACTGAGCATTCTCCTGGTGGGCAGCCTGCAGATAT
GGAAGAAGTTTATCAAGAAGGGTGCACAGATTCCTGTGACTGGCTGAGAAATGAGTGAGGCCTTGAAGATGCCTTCATCA
CCTGTGGAGCACCTTGAAAAACAAGGTATTGATGTGCAGGTGCTCCAGACACAGCAGGCAGTAAGGAATATAATGCCTTG
ATTGCCCAAGGGCTCAGGGTGGAAGTGTTTGGTGCATTCCATTCCACCTGC

Alignment

ORF - retro_lafr_784 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSSPEIASLSWGQMKVRGSTKTYKDCKVWPGG-SRAWDWRETGTEHSPGVQPADVEEV-VKKGVQTLVIG
          M.SPE.A.LSW.Q.KV.GSTKT.KDCKVWPG..S..W..RET.TEHSPG.QPAD.EEV..KKG.Q..V.G
Retrocopy MCSPEMAFLSWEQIKVQGSTKTCKDCKVWPGS<SPVWNQRETRTEHSPGGQPADMEEV>IKKGAQIPVTG

Parental  RGMSEALKVPPSTVEYLEKQGIDVRVLQTEQAV-KEYNALVAQGVRVG--GVFHSTC
          ..MSEALK.P.S.VE.LEKQGIDV.VLQT.QAV.KEYNAL.AQG.RV...G.FHSTC
Retrocopy *EMSEALKMPSSPVEHLEKQGIDVQVLQTQQAV<KEYNALIAQGLRVEVFGAFHSTC

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_784 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002128	1 retrocopy	retro_amel_1604,
Callithrix jacchus	ENSCJAG00000014890	1 retrocopy	retro_cjac_165,
Echinops telfairi	ENSETEG00000006423	1 retrocopy	retro_etel_187,
Felis catus	ENSFCAG00000007450	1 retrocopy	retro_fcat_8,
Loxodonta africana	ENSLAFG00000000518	1 retrocopy	retro_lafr_784 ,
Microcebus murinus	ENSMICG00000000300	2 retrocopies	retro_mmur_157, retro_mmur_424,
Mustela putorius furo	ENSMPUG00000015932	1 retrocopy	retro_mputfur_1468,
Rattus norvegicus	ENSRNOG00000012584	1 retrocopy	retro_rnor_2097,
Tarsius syrichta	ENSTSYG00000002262	1 retrocopy	retro_tsyr_1886,
Tursiops truncatus	ENSTTRG00000007111	1 retrocopy	retro_ttru_406,