RetrogeneDB ID: retro_lafr_591

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:36011934..36012510(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BMI1
• Ensembl ID: ENSLAFG00000016845
• Aliases: None
• Description: None

Sequence

>retro_lafr_591
TGTACGTAAAACATATGTTATGTGTTACCTGCAGACCAGCAAATATTGTCCTGTGATGTCCAAGTTTACAAAACCAGACC
ACCCCTGAACATAAGGTCAGATAAAACTCTTCCATATATGGAACACAAATTAGTTCCAGGCCTTCTAAAAAATGAAACAA
AGAGAAGGGATTTTTATGCAAATCATCTTCAGTTGACGCTGCCAGTGGCTCTAAGGAAAATAGAGAAGTTGCAGGTGAAT
TATAAGAGAATTGTAACTGATGATGAGACAATAAGCTTCTCCACTGCATTTTTTGACCAGAAGAGATTGAATCAGAAAGT
AAACAAAGTCAAAGAGAAATCTAAGGCGGAAGTGAATAATAAAATACATCAGAGATGTCCAGCAGCAATGATTATGATTA
GCCTAAATTTTATTTTAAGGATGTTTCTCAGAAGCAAAACGGACAAACCTAATACTTTCCCAACTGATGTCATGTATGAA
GAGAAATCTTTAAAGGATGACTATACACTAATGGATATCTCCTACATTTATACCTAAAGGAAATATGGGTTTTTTCCTTT
GAAATATAGTCAGAGA

Alignment

ORF - retro_lafr_591 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.24 %
• Parental protein coverage: 65.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CKTCIVHYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAH-PSADAA
          C...I...L........CDVQV.KTRP.LNIRSDKTL.....KLVPGL.KNE.KRR.DFYA.H..S.DAA
Retrocopy CT*NICYVLPADQQILSCDVQVYKTRPPLNIRSDKTLPYMEHKLVPGLLKNETKRR-DFYANH<SSVDAA

Parental  NGSNEDRGEVADE-DKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKA--NDKRYLRCPAAMTVMH--
          .GS.E.R.EVA.E..KRI.TDDE.IS.S..FFDQ.RL..KVNK.KEKSKA..N.K...RCPAAM......
Retrocopy SGSKENR-EVAGE>YKRIVTDDETISFSTAFFDQKRLNQKVNKVKEKSKAEVNNKIHQRCPAAMIMISLN

Parental  --LRKFLRSKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVR
          ..LR.FLRSK.D.PNTF..DVMYEE..LKD.YTLMDI.YIYT.R..G..PLKY..R
Retrocopy FILRMFLRSKTDKPNTFPTDVMYEEKSLKDDYTLMDISYIYT*RKYGFFPLKYSQR

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_591 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
Choloepus hoffmanni	ENSCHOG00000011962	1 retrocopy	retro_chof_709,
Callithrix jacchus	ENSCJAG00000036548	1 retrocopy	retro_cjac_2437,
Cavia porcellus	ENSCPOG00000015427	2 retrocopies	retro_cpor_1209, retro_cpor_546,
Gorilla gorilla	ENSGGOG00000025243	1 retrocopy	retro_ggor_3025,
Loxodonta africana	ENSLAFG00000016845	1 retrocopy	retro_lafr_591 ,
Macaca mulatta	ENSMMUG00000000881	1 retrocopy	retro_mmul_2591,
Mus musculus	ENSMUSG00000026739	1 retrocopy	retro_mmus_3710,
Oryctolagus cuniculus	ENSOCUG00000005420	1 retrocopy	retro_ocun_489,
Tupaia belangeri	ENSTBEG00000015631	1 retrocopy	retro_tbel_2369,