RetrogeneDB ID: retro_lafr_267

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_108:1955379..1956023(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5A
• Ensembl ID: ENSLAFG00000008321
• Aliases: None
• Description: None

Sequence

>retro_lafr_267
CTGGCTAATCGAGGAGCAACAAGACCCAACGGGCCAAATACTGGAAATAAAATATGCCAGTTCAAACTAGTACTTCTGGG
AGAGTCTGCTGTTGGCAATTCAAGCCTAGTGCTTCGTTTCGTGAAGGGCCAATTTCATGAATTTCAGGAGAGGACCATTG
GGCTGCTTTTCTAACCCAGACTGTGTGTCTTGATGACACAACAGTAAAGTTTGAAATATGGGATACAGCTGCTCAAGAGC
GATACCACAGCCTAGCACCAATGTACTAAAGAGGAGCACAAGCAGCCATCTTTGTATATGATATCACAAATGAGGAATCC
TTTGCAAGAGCAAAAGACTGGGTAAAAGAACTTCAGAGGCAAGCAAGTCCTAACATTGTAATAGCTTTATCAGGAAACAA
GGCTGACCTAGCAAATAAAAGAGCTGTAGATTTCCAGGAAGCACAGTCCTATGCAGATGATAACAGTTTATTATTCACGG
AAACATCAGCTAAGACATCAATGAATGTAAATGAAATATTCATGGCAATAGCTAAAAAGTTGCCAAAGAACGAGCCACAG
AATCCAGGAGCCAATTCTACCAGGGGAAAAGGAGTAGACCTTATGGAACCCACACAGCCAACCAGGAGTCAGTGTTGTAG
TAAC

Alignment

ORF - retro_lafr_267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANRGATRPNGPNTGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIG-AAFLTQTVCLDDTTV
          .ANRGATRPNGPNTGNKICQFKLVLLGESAVG.SSLVLRFVKGQFHEFQE.TIG.AAFLTQTVCLDDTTV
Retrocopy LANRGATRPNGPNTGNKICQFKLVLLGESAVGNSSLVLRFVKGQFHEFQERTIG<AAFLTQTVCLDDTTV

Parental  KFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLAN
          KFEIWDTA.QERYHSLAPMY.RGAQAAI.VYDITNEESFARAK.WVKELQRQASPNIVIALSGNKADLAN
Retrocopy KFEIWDTAAQERYHSLAPMY*RGAQAAIFVYDITNEESFARAKDWVKELQRQASPNIVIALSGNKADLAN

Parental  KRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGANSTRGRGVDLTEPTQPTR
          KRAVDFQEAQSYADDNSLLF.ETSAKTSMNVNEIFMAIAKKLPKNEPQNPGANSTRG.GVDL.EPTQPTR
Retrocopy KRAVDFQEAQSYADDNSLLFTETSAKTSMNVNEIFMAIAKKLPKNEPQNPGANSTRGKGVDLMEPTQPTR

Parental  SQCCSN
          SQCCSN
Retrocopy SQCCSN

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_267 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.

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267 ,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,