RetrogeneDB ID: retro_lafr_1170

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:42302775..42303204(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISY1
• Ensembl ID: ENSLAFG00000004015
• Aliases: None
• Description: None

Sequence

>retro_lafr_1170
AGAGAGCTATTTGGAAAAGAACCTCTTCCAAGAAAGGCATGAGCTGAGTTCATGAAGGCAATTGATTTTGAGTACTATAG
TTACTTAGATGAAGACGATGTTACTATTTTGCCTTTGGAACAGGAATATGAAAAGAAACTCAGAGCTGAATTGGTAGAAA
AGTGGAAAACTAAGACAGAGGCCTGGCTTTCAAAAAGAGAAAAAGAAGAGGAGGAGCAGAAGAAAGAGATAAATATCTAT
GCTGTCAACAAGGAAGAGTCTGATAAGGAAGGTGGCCTGGAGAAAGGTGAAGATAGACAGCAGAAGTTCATCACTCAAGT
CCTAGTACCATCACAGCAAGATATTGAGGAGGTGCTCAAAGAAAGAAAGAAGATGGAACTCCTTCAGAAGCATGCAAGTG
AGACCCTGAAGGCCCAGGGTGAAAAAGCC

Alignment

ORF - retro_lafr_1170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.51 %
• Parental protein coverage: 52.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RELFEKEPLPPPRKTRAELMKAIDFEYYGYLDEDDGVIVPLEQEYEKKLRAELVEKWKTEREARLARGEK
          RELF.KEPLP..RK..AE.MKAIDFEYY.YLDEDD..I.PLEQEYEKKLRAELVEKWKT..EA.L...EK
Retrocopy RELFGKEPLP--RKA*AEFMKAIDFEYYSYLDEDDVTILPLEQEYEKKLRAELVEKWKTKTEAWLSKREK

Parental  EEEEEEEEEINIYAVNEEESDEEGGQEKGGEDGQQKFIAHVPVPSQQEIEEALVRRKKMELLQKYASETL
          .EEEE...EINIYAVN.EESD.EGG.EK.GED.QQKFI..V.VPSQQ.IEE.L..RKKMELLQK.ASETL
Retrocopy -EEEEQKKEINIYAVNKEESDKEGGLEK-GEDRQQKFITQVLVPSQQDIEEVLKERKKMELLQKHASETL

Parental  QAQSEEA
          .AQ.E.A
Retrocopy KAQGEKA

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_1170 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006886	1 retrocopy	retro_dord_331,
Ficedula albicollis	ENSFALG00000000023	1 retrocopy	retro_falb_5,
Loxodonta africana	ENSLAFG00000004015	2 retrocopies	retro_lafr_1070, retro_lafr_1170 ,
Myotis lucifugus	ENSMLUG00000011804	1 retrocopy	retro_mluc_1401,
Oryctolagus cuniculus	ENSOCUG00000003923	1 retrocopy	retro_ocun_1485,
Taeniopygia guttata	ENSTGUG00000003998	1 retrocopy	retro_tgut_5,