RetrogeneDB ID: retro_lafr_1049

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_61:5984465..5984914(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2G2
• Ensembl ID: ENSLAFG00000001963
• Aliases: None
• Description: None

Sequence

>retro_lafr_1049
CAATTGACACCGAACCCACTAGAAGGAACTGTGGCAGGCCCCGTGAATGAAGGTTTTTTTTGGAATAGGAGCCCTTGATC
ATGGACCCAGAACATACTTGCTTTGAGTTTGGTGTTTTTCCTATCGTCTTGCGTTTTCCACTTGATTACTTCTTAAATTC
CCCAAAGATGAGATTTACCTGTGAAATGTTTCATCCCAACATCAACCCTGACGGGAGGGTCTACATCTCCATCCTGCAAG
CCTGAGTCGACCCCCTAGGGTAAGAGAGCAGCTCCGAGATGCGGAGCCCTGTGCAAAGCCTGGAGAAGATCCTGCTGTTG
GTGGTGAGGGTGCTTTCAGAGCCCAAGGACAAGTGCAGCACCCATGTACATGCTTCCAAAATGTGGTGGGAGGACCCAGA
GCAGTTTTATAAGGTGGCCAAGCCGATGGTACAGAAGCCTCTGGTGCTC

Alignment

ORF - retro_lafr_1049 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.11 %
• Parental protein coverage: 91.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELTLNPPEGIVAGPMNE-ENFFEWEALIMGPEDTCFEFGVFPAILSFPLDYPLSPPKMRFTCEMFHPNIY
          .LT.NP.EG.VAGP.NE...F.E.E.LIM.PE.TCFEFGVFP..L.FPLDY.L..PKMRFTCEMFHPNI.
Retrocopy QLTPNPLEGTVAGPVNE<RFFLE*EPLIMDPEHTCFEFGVFPIVLRFPLDYFLNSPKMRFTCEMFHPNIN

Parental  PDGRVCISILHAPGDDPMGYESSAERWSPVQSVEKILLSVVSMLAEPNDESGANVDASKMWRDDREQFYK
          PDGRV.ISIL.A...DP.G.ESS.E..SPVQS.EKILL.VV..L.EP.D.....V.ASKMW..D.EQFYK
Retrocopy PDGRVYISILQA-*VDPLG*ESSSEMRSPVQSLEKILLLVVRVLSEPKDKCSTHVHASKMWWEDPEQFYK

Parental  IAKQIVQKSLGL
          .AK..VQK.L.L
Retrocopy VAKPMVQKPLVL

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_1049 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000001963	1 retrocopy	retro_lafr_1049 ,
Ictidomys tridecemlineatus	ENSSTOG00000007968	1 retrocopy	retro_itri_1338,