RetrogeneDB ID: retro_lafr_1052

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_61:13713852..13714586(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMM21
• Ensembl ID: ENSLAFG00000018631
• Aliases: None
• Description: None

Sequence

>retro_lafr_1052
ATGATTTTCACTCTTCTGCGAGGTATGTAGCATACGGAGAAGGTGCACAGGTGTGCAGGGGCGCGACTGTTTTGGCCCCA
CTTCTTGCTTAACAAAGCTTGCTTGAATACTGAGCCCAGCATGAAATGGGGGCTGCCAGAGCAGAATAAAACTGTTCAGC
CCAGGGGTATCCTTGGGGTCACCCCAAGAACTCTCTAGAGGTAGGGACGGAGACTCCGGAGAGTGAAGGAGGATGGCAGC
AAACAAATGTCTGTGCACAGAAGTCCGAGAGGGGAGATCGCTGTCTCGATGTCACAGAAAGTGAAAGAAGGTGGAAGAGA
TTTTACCTACTTAATAGTATTGCTTTTTGAAGTCAGCATGACAGGTAGCTTGTTTTACCTGATTTTTAGAGAAATTTTCT
TTTCATCCAGCCCTAATTAGATACATGGGAAAGCCTTAGAGAAATGCAGATTACATCCCAAGGTGATAGATGTTTTTGGT
GAGCTGATCAAAGGCTATGGGGAGATGGTACCATGTGGGAGAAGGCGGCATGTCAGTTTCATCGAGCACGTTGAAGACTG
GCTGCACATATGTGACTCAAGTTCTACAAAGAGGGCTTGGAGCCGGGGAAGCACCAGACCGTGGACCTGGAAGTAAAGGA
GAACCCAGAAAGTAGCGAATATGAATTCTGATACATTTTTGTAGAAGGTGAAGCCTACCCTAGAAGAACTATTGTCATTG
AAGACAGTCGATCC

Alignment

ORF - retro_lafr_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MICTLLRAVQHTEKLHRSPAARLCWPHFVLNKASLRTEPSLKWWLPEQNKTVRPRGILGVIPRTIWTQGR
          MI.TLLR...HTEK.HR...ARL.WPHF.LNKA.L.TEPS.KW.LPEQNKTV.PRGILGV.PRT....GR
Retrocopy MIFTLLRGM*HTEKVHRCAGARLFWPHFLLNKACLNTEPSMKWGLPEQNKTVQPRGILGVTPRTL*R*GR

Parental  GLQRAKEDGSKQVPVHRSPRRETDVSTSQKVKEAGRDFTYLIVVLIGISITGGLFYVIFRELFSSGSPSK
          .L.R.KEDGSKQ..VHRSPR.E..VS.SQKVKE.GRDFTYLIV.L...S.TG.LFY.IFRE.F.S.SP..
Retrocopy RLRRVKEDGSKQMSVHRSPRGEIAVSMSQKVKEGGRDFTYLIVLLFEVSMTGSLFYLIFREIFFSSSPN*

Parental  IYGKALEKCRSHPEVIGVFGEPIKGYGEMTRRGRRHHVSFIEYVKDGLR-HMRLKFYIEGSEPGKHGTVH
          I.GKALEKCR.HP.VI.VFGE.IKGYGEM...GRR.HVSFIE.V.D.L..HM.LKFY.EG.EPGKH.TV.
Retrocopy IHGKALEKCRLHPKVIDVFGELIKGYGEMVPCGRRRHVSFIEHVEDWLH<HM*LKFYKEGLEPGKHQTVD

Parental  VEVKENPESGGYEFHYIFVEVEAYPGRMIVIEDNRS
          .EVKENPES..YEF.YIFVE.EAYP.R.IVIED.RS
Retrocopy LEVKENPESSEYEF*YIFVEGEAYPRRTIVIEDSRS

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_1052 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000018631	1 retrocopy	retro_lafr_1052 ,