RetrogeneDB ID: retro_lafr_403

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:3436854..3437656(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGK
• Ensembl ID: ENSLAFG00000002479
• Aliases: None
• Description: None

Sequence

>retro_lafr_403
GGATGCATATAGCTGAATAGCATTACCCTACACAGTCGTACCCTCTTTGCCAAAAGTGGAAACAAAATCCAACATATTAC
AGATACTACCCTAGCCACTGCGAAAGGACAGACGATTCCACTTGATGTCTTGCAGATTAAGCGTGAAAAAGAGCAGCCCC
TGTTTGCAATGACCGGCCTTCGATGGGGGTTCTTCCGGGAAGCCAGCGTCAAAGTCAGCAAGTACTGCTATCTTTGGCCT
CTAAAAACCAAAGCAGCCCAGTGTTTCAACACTCTTAAGGAGTGGCCGCATTCTCACCAGGCCTCCATCTCCTATAAGGG
ACCCACAGGGAGACCCTCTGAGGAGCCTTGGAGAGGCCCCTCCGCGCCCAAGTCTGTATTGGAAGATTCTGCGGAGGCTG
GCGTCCTACTGAGCAAAGTGGCAGGCACCCCCTCTCGAGAGGTGTGCCCCAAGGATTGAGAGGTGCAGTGGTCCACCACT
GAGCTGTCCATCACAACAGGCAACGAGGGGCTCGACCTGGCGAGCACCAAGGACTCCATGAACTTCTGCAACGAACCCAA
CAGGGTCTGCAAAGGAGACTTCACAATTATTGGTAGCAAGAGGCTGCCCGACCCTGCCCTGTGTCTCGCAGCACCGACTG
TCTGTAAGCTGCACGTGCAAGCTGCTGCTGCCCAAGGTAGCAGGGGGCTCCTTCAGTATCCACAGCGAAGGCTCGGAGGT
GAGGCCAGTGGAGGTGATGCTGCTCCACCACAAGATGCGCTTCTTCTGTGACCTGAGAAAGCCAGAGCAGGTGCTTGCGG
GC

Alignment

ORF - retro_lafr_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.51 %
• Parental protein coverage: 63.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GFIPLGQTSSLSQTLFAKSGNKVQHITDATLAIVKGETVPLDVLQIKKNEKQPVRAIKRL-LGQFPRQGT
          G.I.L......S.TLFAKSGNK.QHITD.TLA..KG.T.PLDVLQIK....QP..A...L..G.F.....
Retrocopy GCI*LNSITLHSRTLFAKSGNKIQHITDTTLATAKGQTIPLDVLQIKREKEQPLFAMTGLRWGFFREASV

Parental  PCSEHWFMRPSVPNAVSFYSSQQEWPQTHQASISYTGPTQRPSSEP-EEAPPRPSLYRRILRRLASYWAQ
          ..S......P....A........EWP..HQASISY.GPT.RPS.EP..EAPPRPSLY..ILRRLASY.A.
Retrocopy KVSKYCYLWPLKTKAAQCFNTLKEWPHSHQASISYKGPTGRPSEEP>GEAPPRPSLYWKILRRLASY*AK

Parental  PQ-DAPSREVRPEVWKELQLSTIELSITTRNQQLDLASPEDFMTICIEPDTVSKGDFITIGSKRMRDPTL
          .Q...PSREV.P....E.Q.ST.ELSITT.N..LDLAS..D.M..C.EP..V.KGDF..IGSKR..DP.L
Retrocopy WQ<GTPSREVCPKD-*EVQWSTTELSITTGNEGLDLASTKDSMNFCNEPNRVCKGDFTIIGSKRLPDPAL

Parental  CLA-GTECLQASK-CTLLLPQGAGGSFSIDSEEYEAMPVEVTLLPRKLHFFCDPRKREQMLRG
          CLA..T.CL.A...C.LLLP..AGGSFSI.SE..E..PVEV.LL..K..FFCD.RK.EQ.L.G
Retrocopy CLA<STDCL*AAR<CKLLLPKVAGGSFSIHSEGSEVRPVEVMLLHHKMRFFCDLRKPEQVLAG

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_403 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013589	1 retrocopy	retro_cjac_3228,
Gorilla gorilla	ENSGGOG00000008821	1 retrocopy	retro_ggor_3061,
Loxodonta africana	ENSLAFG00000002479	1 retrocopy	retro_lafr_403 ,
Microcebus murinus	ENSMICG00000002561	1 retrocopy	retro_mmur_850,
Macaca mulatta	ENSMMUG00000021017	1 retrocopy	retro_mmul_2637,
Mus musculus	ENSMUSG00000029916	1 retrocopy	retro_mmus_1130,
Nomascus leucogenys	ENSNLEG00000002291	1 retrocopy	retro_nleu_2349,
Pongo abelii	ENSPPYG00000018064	1 retrocopy	retro_pabe_3812,
Pan troglodytes	ENSPTRG00000019775	2 retrocopies	retro_ptro_3269, retro_ptro_3311,