RetrogeneDB ID: retro_lafr_711

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_32:9646841..9647616(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBLL1
• Ensembl ID: ENSLAFG00000029522
• Aliases: None
• Description: None

Sequence

>retro_lafr_711
CCTGCGAGCGGAATCATGGAGCGTCCTGAGGGGATCGGTTGTAATGAAGAAGAGGGAGGGTATGACTCTAGTGGGGGTGA
ACCACGTAGAAATCAGCAAAGATTTATTCAAAGCGTTTTTTGGGATTTTCAGATAAACATCTTAGGTGAAAAGGATGGAT
ACGCCAATTCATTTCTGTGGTGGATGTGAATTACCGATTAAAATCTATGGGCGGATGATACCATGCAAGCATGCTTTTTG
CTATAAATGTGCTATTTCACATGGAAAAAAGCGAGATGAGGTGTGTCCAGAATGTAGCAATCCCGTGATGCGAATTGAGA
AGCATCCACAAGGTTCTATCTTCATGTGTATCACTGTTCAAGGATGCAAGAGAACATACTTGTCTCAAAGAGACTTAGAG
GCTCATATCAACTTCCGCCATTTAAGAGATGGAAAACCTGTTACCAGTGTTTAACTTGAAATTGTTCATCCTTCGTATTG
CTCTACCACCAAACTGAAACCTCTAATTGTTTTACAATGTTGCCAGACAAGCACCATATGAACTGTATCCTGCCAAAGCA
GCACTTCGTGCTACCACTACCTCCGTTGCAACATGATCCAATGATCAGCCACATGAGGATATCTGTGTTCTTCCAGTGGA
ATTGCCCACAGCTCCGTCTCCAACTTCACCTCCTTCCAAGTCAGTAAACTGAGTCAGGAAACCTTTCAGATTTCAACAAC
AAAACATGACAATCTAATAACTGTCTCTTTTTAGGATGATTTAAATTCAGGTGCT

Alignment

ORF - retro_lafr_711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.53 %
• Parental protein coverage: 65.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PAKAPTGDEEGFNYNEEER-YDCKGGEHFGNQRRFPGHLFWDFQINILGEKD-DTPVHFCDKCGLPIKIY
          PA.......EG...NEEE..YD..GGE...NQ.RF....FWDFQINILGEKD.DTP.HFC..C.LPIKIY
Retrocopy PASGIMERPEGIGCNEEEGGYDSSGGEPRRNQQRFIQSVFWDFQINILGEKD>DTPIHFCGGCELPIKIY

Parental  GRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHR
          GRMIPCKH.FCY.CAI.H.KK.D..CP.CS.PV.RIE....GS.FMC..VQGCKRTYLSQRDL.AHIN.R
Retrocopy GRMIPCKHAFCYKCAISHGKKRDEVCPECSNPVMRIEKHPQGSIFMCITVQGCKRTYLSQRDLEAHINFR

Parental  HMRAGKPVTRASLENVHPT-IAPPP-TEIPDRFIMPPDKHHMSHIPPKQHIMMPPPPLQHVPHEHY-NQP
          H.R.GKPVT...LE.VHP..IA.PP.TE....F.M.PDKHHM..I.PKQH......PL....H.....QP
Retrocopy HLRDGKPVTSV*LEIVHPS>IALPP>TETSNCFTMLPDKHHMNCILPKQHFVL---PLPPLQHDPM<DQP

Parental  HEDIRAPPAELSMAP----PPPRSVS--QETFR-ISTRKHSNLITVPIQDDSNSGA
          HEDI...P.EL..AP....PP..SV......FR.IST.KH.NLITV...DD.NSGA
Retrocopy HEDICVLPVELPTAPSPTSPPSKSVN*VRKPFR<ISTTKHDNLITVSF*DDLNSGA

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_711 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031990	1 retrocopy	retro_cfam_2047,
Loxodonta africana	ENSLAFG00000029522	1 retrocopy	retro_lafr_711 ,
Pteropus vampyrus	ENSPVAG00000000781	1 retrocopy	retro_pvam_1043,