RetrogeneDB ID: retro_lafr_931

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:99571075..99571643(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED27
• Ensembl ID: ENSLAFG00000011556
• Aliases: None
• Description: None

Sequence

>retro_lafr_931
GTGGATCCTGTGCAGGACAAAACTCCTCTCTGTAGTCAGCTCCTTCAAGCATATAAATGGTCAAACAAGTTGCAGTACCA
CGCAGGTCTAGCATCTGGCCTTTTGAATTGACAGTTGTTGAAACATTCTGCTAACCATGTGGGAGTATCTGCTAAACAGA
CAAAAGGCTCAACCCGCGACTCTTGTCTTACCTCCTCAGTATGTTGATGATGTGATCAGCCACACTGACAAGATGTTTCC
TGAAGTGTCAGTCCACTTACCCAGACCCAATGGAACCTCAGCAATGCATCTGGTGACTTTGGGAAAGGTGTTGAAAGTGA
TTGTCATCATGTGGAGCGTATTCATTGATGGAACAATGGTAAAGGGATATAACAAAAATGTTTACAAAGATGGCAAGCTT
GATGTATGGTCCAAATCTAACTATCAAGTGTTCCAAAAGGTGACAGACCATGCCACTAGTGCCGTGCTTCACTATCAGTT
GTCCCAGATTCCAGACGTCGTGGTCAGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTTCAGGCCCCATGCC
AACGCTGC

Alignment

ORF - retro_lafr_931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.69 %
• Parental protein coverage: 61.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDPVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQQSLKRSANQMGVSAK-RRPKAQPTTLVLPPQYV
          .DPVQDKTPL.SQLLQAYKWSNKLQYHAGLASGLLN.Q.LK.SAN..GVSAK.R......T....P.QYV
Retrocopy VDPVQDKTPLCSQLLQAYKWSNKLQYHAGLASGLLN*QLLKHSANHVGVSAK>RQKAQPATLVLPP-QYV

Parental  DDVISRIDRMFPEMSIHLSRPNGTSAMLLVTLGKVLKVIVVMRSLFIDRTIVKGYNENVYTEDGKLDIWS
          DDVIS..D.MFPE.S.HL.RPNGTSAM.LVTLGKVLKVIV.M.S.FID.T.VKGYN.NVY..DGKLD.WS
Retrocopy DDVISHTDKMFPEVSVHLPRPNGTSAMHLVTLGKVLKVIVIMWSVFIDGTMVKGYNKNVY-KDGKLDVWS

Parental  KSNYQVFQKVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQAPCQRC
          KSNYQVFQKVTDHAT.A.LHYQL.Q.PDVVVRSFMTWLRSYIKLFQAPCQRC
Retrocopy KSNYQVFQKVTDHATSAVLHYQLSQIPDVVVRSFMTWLRSYIKLFQAPCQRC

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_931 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160563	1 retrocopy	retro_hsap_3342,
Gorilla gorilla	ENSGGOG00000010390	1 retrocopy	retro_ggor_130,
Loxodonta africana	ENSLAFG00000011556	1 retrocopy	retro_lafr_931 ,
Myotis lucifugus	ENSMLUG00000000364	1 retrocopy	retro_mluc_243,
Nomascus leucogenys	ENSNLEG00000012828	1 retrocopy	retro_nleu_115,
Pongo abelii	ENSPPYG00000019706	1 retrocopy	retro_pabe_109,
Pan troglodytes	ENSPTRG00000021492	1 retrocopy	retro_ptro_87,