RetrogeneDB ID: retro_lafr_680

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_3:56315248..56315857(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNDBP1
• Ensembl ID: ENSLAFG00000004497
• Aliases: None
• Description: None

Sequence

>retro_lafr_680
GGTGCCATTCTGGACATTGTGGATGGCATGGCTTAGCTCTTGAAGTGCTTTTCATCTCTCTGTCTCAGAGCCCTGAAAGC
AAGGGCCCTATTTTTTCTGCAACACTGTTTGGGTTATCTGCCAGCAGGTACCTCTGATACCAAGAAATAATAAAGCTGCA
ATCCTTTTAATGTTGATGAAGAGTGTAAATTTTGTGAAGGATGCACATGAGGAGAAAAAGGGGGCTGTGGAAGAATGTGA
CCCTTACTCTGGCCACTTGAATAACTCTGAGGAAGACAGCTTGGGGAATGACCATTATATGGACCCTGATGTTGAGGAGG
ATGCATTGGAGTTTCTAAACAATCAGGATTATACTGATCAGAGGAAGATCAGGAGCTCATAATCCCATGCATTTTGCTGG
TGAAAGCATCCAAAGCCAGCCTTGTGAAAATCCGGATCTCAGTGACAGAGAATGGGAAGAAAGACCAGGAGGCTCAGCTG
GATGACGTTGTGGATATTTCTGATGAGATCAGCCCCAGTGTGAATGATTTGGTTCTGAGCATATATCCATCGATGTGCCA
CCCGACTGTGTGAATCAACTGTGTGAAACTTGCATCTGTTTTAAAGAAA

Alignment

ORF - retro_lafr_680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.38 %
• Parental protein coverage: 56.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSILDIVDGMTQLVE-ALLITPSQSPENKDLIFCNTVWVACQQVPRIPRDNKAAALLMLTKSVNFVKDAH
          G.ILDIVDGM..L...A.....S.........FCNTVWV.CQQVP.IPR.NKAA.LLML.KSVNFVKDAH
Retrocopy GAILDIVDGMA*LLK>AFHLSVSEP*KQGPYFFCNTVWVICQQVPLIPRNNKAAILLMLMKSVNFVKDAH

Parental  EEMERAVEECDPYSGLLN--EEDNLVNDHRVDSDGHNDAEEDALGFPNNRD-VYWSEEDQELIVPCLALV
          EE...AVEECDPYSG.LN..EED.L.NDH..D.....D.EEDAL.F.NN.D..Y.SEEDQELI.PC..LV
Retrocopy EEKKGAVEECDPYSGHLNNSEEDSLGNDHYMDP----DVEEDALEFLNNQD<LY*SEEDQELIIPCILLV

Parental  KASKASLKKIRISVAENGKKDQVAQLDDIVDISDEISPSVDDLALSIYPPVCHLTVRISSAKLVSVLKK
          KASKASL.KIRISV.ENGKKDQ.AQLDD.VDISDEISPSV.DL.LSIYP..CH.TV.I...KL.SVLKK
Retrocopy KASKASLVKIRISVTENGKKDQEAQLDDVVDISDEISPSVNDLVLSIYPSMCHPTV*INCVKLASVLKK

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_680 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012594	2 retrocopies	retro_chof_1251, retro_chof_1832,
Loxodonta africana	ENSLAFG00000004497	1 retrocopy	retro_lafr_680 ,
Otolemur garnettii	ENSOGAG00000011162	1 retrocopy	retro_ogar_1358,