RetrogeneDB ID: retro_lafr_935

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:39879541..39880057(-)
• Located in intron of: ENSLAFG00000015187

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAMM41
• Ensembl ID: ENSLAFG00000011239
• Aliases: None
• Description: None

Sequence

>retro_lafr_935
GCTGCTTTTCTACTGCTCCCCGAAAGCTTTTCGGAAGAAGAACTCTTTATAGAGATTGCAGGACTCTCCTATTCAGGTGA
CTTTCGGATGATGGTTGGAGAGGATAAGTCAAAAGTGTTGAATATCGTGAAGCCCAACGTAGTTCACTTTCGTGAACTTT
ATGGCACCATACTACAGGAGAATCCCCAAGTGGTGTATAAAATAAAGCAAGGCAGACTGGAGCTAGATAAGAGCCCAGGA
CAATTCACTCAGCTAATGGCACTGCCCAAAACCTTACAGCAATGAAGAAATCATATTATGGGCCCTCCTGGAAAAAACAG
AAATGTGGAAGAAACTTTATTTCAACTTGCTAACAATCCTGACTGTTCAGAGGTGGTGCGCCTAGGCCTTTCAGCAATCG
TCAGACCCTCCAGTGTGAGACAGAGCACCAAGGGCAATTTTACTGCTGGCATGAAGAAATCGGTGATTTATAGTTCATTA
AAACTACACAAAATGTGGAGAGGATGGCTGAGGAAA

Alignment

ORF - retro_lafr_935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.64 %
• Parental protein coverage: 51.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAFLLLPESFSEEELFIEIAGLSYSGDFRMMVGEDKSKVLNIVKPNVVHFRELYGTILQENPQVVYKIQQ
          AAFLLLPESFSEEELFIEIAGLSYSGDFRMMVGEDKSKVLNIVKPNVVHFRELYGTILQENPQVVYKI.Q
Retrocopy AAFLLLPESFSEEELFIEIAGLSYSGDFRMMVGEDKSKVLNIVKPNVVHFRELYGTILQENPQVVYKIKQ

Parental  GRLELDKSPEGQFTQLMALPKTLQQRINHIMDPPGKNRDVEETLLQLANDPDCSEVVRLGLSAIVRPSSM
          GRLELDKSP.GQFTQLMALPKTLQQ..NHIM.PPGKNR.VEETL.QLAN.PDCSEVVRLGLSAIVRPSS.
Retrocopy GRLELDKSP-GQFTQLMALPKTLQQ*RNHIMGPPGKNRNVEETLFQLANNPDCSEVVRLGLSAIVRPSSV

Parental  RQSTKGIFTAGMKKSVIYSSLKLHKMWRGWLSK
          RQSTKG.FTAGMKKSVIYSSLKLHKMWRGWL.K
Retrocopy RQSTKGNFTAGMKKSVIYSSLKLHKMWRGWLRK

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_935 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000011239	1 retrocopy	retro_lafr_935 ,
Monodelphis domestica	ENSMODG00000006153	1 retrocopy	retro_mdom_556,