RetrogeneDB ID: retro_lafr_1248

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_96:2020084..2020881(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F4
• Ensembl ID: ENSLAFG00000026216
• Aliases: None
• Description: None

Sequence

>retro_lafr_1248
CTGGAAGGTATCGGGCTGGTAGAGAACAAATCCAGGAATAGCAACCAGTGGAAGGTCGTAGGCCTGGCTGCATACCTGGG
AGGCTGCGGATGAGCTGACCGGGCTCAAGGCAGAGATGGAGGAGCTGCAGTGGCGGGAATAAGAACTGGACCAGCACAAG
GCGTGGGCACAGCAGAGCACCCAGAATGCCACAGAGGACGTACAGAACAGCTGCGTGGCCTACGTGACTCGTGAGGACAT
CTGCAGATGCTTTGCTGGAGATGCCCTCCTGGCCATCTGGCCCATCAGGCACCAGCCTGGAGTGCCCATCCCAGAGGACC
TCAGGGGCAGAAGGAGCACCAGGTTCCCCTGAAGAGTGTGAGTGGTCCCCTCGAAGTGCTGCTGGTGAGCAAGCGGGCAT
GGAGCTCACCGCCTGTGGCTGTGCCTGTGCCACCCCCCGAACATCTGCCCCAGGGCCCACCTGCTGACTCTATCCCTCTG
TCTCTGCCCAAGCCTACCCTGGCCCAGCCTCAGGGAGCCTCACGCTCAAGCAGTCCCCAGCTGACCACCCCTTTCCCTGT
CCCTAGCAGCATTAAGGCCCAGGGGGCAGCCGGCCCAACAGCTGAGAGCACAGTAAGAGGCAACCCTGGCACCGACAGCA
GGGACAGTGGCAAGCTCAGCTCACTTCCTCTGGGCCCCACAGCACTGGACACCTGGCCACTGCAGTCTTCTGCCCTCCTG
GGCAGCAATAGCAATGGCAGTTCATCCAGACCCAACCTCCTACCTCCTGTGAGCCCATCAAAGCAGACTCCACTGGC

Alignment

ORF - retro_lafr_1248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 66.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LEGIGLIEKKSKNSIQWKGVG-PGC-NTREIADKLIELKAEIEELQQREQELDQHKVWVQQSIRNVTEDV
          LEGIGL.E.KS.NS.QWK.VG.PGC..T.E.AD.L..LKAE.EELQ.RE.ELDQHK.W.QQS..N.TEDV
Retrocopy LEGIGLVENKSRNSNQWKVVG<PGC<HTWEAADELTGLKAEMEELQWRE*ELDQHKAWAQQSTQNATEDV

Parental  QNSPHTLAYVTHEDICRCFAGDTLLAIRAPSGTSLEVPIPE-GLNGQKKYQIHLKSVSGPIEVLLVNKEA
          QNS....AYVT.EDICRCFAGD.LLAI..P......VPIPE.G..GQK..Q..LKSVSGP.EVLLV.K.A
Retrocopy QNS--CVAYVTREDICRCFAGDALLAI-WPIRHQPGVPIPE<GPQGQKEHQVPLKSVSGPLEVLLVSKRA

Parental  WSSPPVAVPVPPPEDLLQGPPAVSTPPPLPKPTLAQAQEASRPSSPQLAMPAPVPSSVEAQGVASPVAES
          WSSPPVAVPVPPPE.L.QGPPA.S.P..LPKPTLAQ.Q.ASR.SSPQL..P.PVPSS..AQG.A.P.AES
Retrocopy WSSPPVAVPVPPPEHLPQGPPADSIPLSLPKPTLAQPQGASRSSSPQLTTPFPVPSSIKAQGAAGPTAES

Parental  TVRGGPGTDSKDSGELSSLPLGPTALDTRPLQSSALLDSSSNSSSSGSN-PSTSFEPIKADSTG
          TVRG.PGTDS.DSG.LSSLPLGPTALDT.PLQSSALL.S.SN.SSS..N.P.TS.EPIKADSTG
Retrocopy TVRGNPGTDSRDSGKLSSLPLGPTALDTWPLQSSALLGSNSNGSSSRPN<PPTSCEPIKADSTG

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_1248 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	ENSLAFG00000026216	1 retrocopy	retro_lafr_1248 ,
Tursiops truncatus	ENSTTRG00000010268	1 retrocopy	retro_ttru_1583,