RetrogeneDB ID: retro_lafr_767

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_37:4868553..4868931(+)
• Located in intron of: ENSLAFG00000015901

Retrocopy information

• Ensembl ID: ENSLAFG00000031300
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LRRC57
• Ensembl ID: ENSLAFG00000005465
• Aliases: None
• Description: None

Sequence

>retro_lafr_767
CGAGCAGACTGTGAGGTGAGGGGTAGGATGGGGAACAGTGGCCTCCACATTCATGTGGAGACCAAGCAGAAAACGGGTGT
CTTTCAGCTCAAAGACTGTGGGCTGACCAAGTTCCCCTCAGAGTTGCAGACGCTGACGAGCAACCTCAGGACTGTCGACT
TGTCCAAGAACATCAAGAGACCTCAGCCTATCCTGATAGGGAAGTCCACTCTGCTGAAGAACCTCTCCCTCAACAACAAA
CTAATTGTTCTACCTGATGTGCTGTGCAATCTGAAAAAACTAGAAATACTAAGCCTAAACAACAATCACCTGGTACAGCT
ACCATGGCCCTTTGGGCAACTCTCCGCTCTCAAGACGCTGAGCCTCTCTGGGAACCAA

Alignment

ORF - retro_lafr_767 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.44 %
• Parental protein coverage: 51.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRNLNCGARMGNSALRAHVETAQKTGVFQLKDRGLTEFPSELQKLTSNLRTIDLSNNKIESLPPMLIGKF
          R.......RMGNS.L..HVET.QKTGVFQLKD.GLT.FPSELQ.LTSNLRT.DLS.N.I....P.LIGK.
Retrocopy RADCEVRGRMGNSGLHIHVETKQKTGVFQLKDCGLTKFPSELQTLTSNLRTVDLSKN-IKRPQPILIGKS

Parental  ALLKSLSLNNNKLTVLPDELCNLKKLEMLSLNNNHLTELPSTFGQLSALKTLSLSGNR
          .LLK.LSLNN.KL.VLPD.LCNLKKLE.LSLNNNHL..LP..FGQLSALKTLSLSGN.
Retrocopy TLLKNLSLNN-KLIVLPDVLCNLKKLEILSLNNNHLVQLPWPFGQLSALKTLSLSGNQ

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_767 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006482	1 retrocopy	retro_chof_2306,
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819,
Homo sapiens	ENSG00000180979	1 retrocopy	retro_hsap_2163,
Gorilla gorilla	ENSGGOG00000009597	1 retrocopy	retro_ggor_1718,
Loxodonta africana	ENSLAFG00000005465	2 retrocopies	retro_lafr_1027, retro_lafr_767 ,
Macaca mulatta	ENSMMUG00000001544	1 retrocopy	retro_mmul_901,
Nomascus leucogenys	ENSNLEG00000004485	1 retrocopy	retro_nleu_1812,
Otolemur garnettii	ENSOGAG00000007751	1 retrocopy	retro_ogar_3437,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649, retro_ptro_1650,
Rattus norvegicus	ENSRNOG00000009143	1 retrocopy	retro_rnor_796,
Rattus norvegicus	ENSRNOG00000048310	1 retrocopy	retro_rnor_1732,