RetrogeneDB ID: retro_lafr_233

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:58961068..58961456(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCL2L2-PABPN1
• Ensembl ID: ENSLAFG00000031227
• Aliases: None
• Description: None

Sequence

>retro_lafr_233
GGCAATGTGGAGTATGGTGCAACAGCGGAAGAGCCGGAAGCAAACTTTCATGGCTGTGATTCAGTCAACCGTGTTACCCT
GCTCTGTGACAAATTCAGTGGCCATCCCAAAGAGTTTGCATATATAGAGTTCTCAGACGAGGAGTCAGTGAGGACGTCCT
TGCCTTAGATGAGTCATTTTTTAGAGGAGGACAAATCAAGGTGATCCCAAAATGAACCAAAGACCAGGCATCGGCAAAAT
AGACTGGGGTTTTCAACGAGTACCCTACCATGCCCTGACCTCCAACTCCAACCGTTCCGGCTCTTGATTCTACAGTGCTT
TCAACAGCAGGCCCTGGTGTCACGTCTACTGGTGCCAGGCTAAAGCAGCATCATGGTATTCCCCTTAC

Alignment

ORF - retro_lafr_233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.97 %
• Parental protein coverage: 86.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-LALDESLFRGRQIKVT
          GNV.YGATAEE.EA.FHGC.SVNRVT.LCDKFSGHPK.FAYIEFSD.ESVRTS.LALDES.FRG.QIKV.
Retrocopy GNVEYGATAEEPEANFHGCDSVNRVTLLCDKFSGHPKEFAYIEFSDEESVRTS<LALDESFFRGGQIKVI

Parental  PKRT-NRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRVYRGRARATSWYSPY
          PK.T..RPGI...D.GF.R..Y.A.T.N.N.S.S.FYS.FNSRP...VY...A.A.SWYSPY
Retrocopy PK*T<QRPGIGKIDWGFQRVPYHALTSNSNRSGS*FYSAFNSRPWCHVYWCQAKAASWYSPY

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_233 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Loxodonta africana	ENSLAFG00000031227	2 retrocopies	retro_lafr_1031, retro_lafr_233 ,
Macaca mulatta	ENSMMUG00000014747	1 retrocopy	retro_mmul_2594,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,