RetrogeneDB ID: retro_lafr_272

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_11:20638107..20638934(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000031297
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CYP51A1
• Ensembl ID: ENSLAFG00000000066
• Aliases: None
• Description: None

Sequence

>retro_lafr_272
ATGGTGTTGCCGGGCTTATTGAAGGTGGGCAAGTAGGTGCTAGGGCAGGCAATGGAGCAGGTGACGGGTGGCAGCCTCCT
TTCTATGTACCTCATCCCCTGCACCTTCAGCCTCAGCCTGGTCTACCTGTTCCACCTCCCCGTTGTCCACCTGGCCCAGC
TGAAGGAGGGGGCGAAAAGTCCACCATACATTTTCTCTCCAATTCCATTCCTTGGACATGCAGTAGCATTTGGGAAAAGT
CCAGTTGAATTCCTAGAAAATGCATATGAGAAGTATGGACCGGTGTTTAGTTTTACCATGGTGAGCAAGACCTTTACTTC
CCTTCTGGGGAGCTATGCTGCTGCACTGTTTTTTACTAGTAAAAATGAAGATATGAATGTAGAAGTTGTCTACAGTCATC
TGACAACACCTACGTGTGGAAAGGGGGTCACATACGATGTGCCTAATCCATTTTTTTTTTAAGCAGAAGAAAACGTTAAA
AAGTGGCCTCGACTTAGCCCCTTTTAGACAGCAGCCTTCTGTAATAGAAAAAGAAACAAAAGAATACTTTGAAAGTTGGG
GGGGAAAGTGGGAAAAAAATTGTTTGAAGCTCTTTCTGAGCTAATAATTTTAATGGCTGCCATTGTTTACATGGAAAGGA
AATCAGAAGTCACCTCAATGAGAAGGTGGAACAGCTGTATGCAGATTCGGATGGAGCTTTTAGCCATGCAGCCTGGCTGT
TGCCTGGTTGGCTGCCTTTGCCAAGTTTCAGATGCAGGGACAGAGCTCATCGAGAGATCAAGAATATTTCCTACAAGGCA
ATCCAGAAATGCAGTCAGGGGAAAAAA

Alignment

ORF - retro_lafr_272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.14 %
• Parental protein coverage: 54.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALLGLLQAGGSVLGQAMEQVTGGSLLSVLLIACTFTLSLVYLFRRAVGHLAQLPAGAKSPPYIFSPVPF
          M.L.GLL..G..VLGQAMEQVTGGSLLS..LI.CTF.LSLVYLF...V.HLAQL..GAKSPPYIFSP.PF
Retrocopy MVLPGLLKVGK*VLGQAMEQVTGGSLLSMYLIPCTFSLSLVYLFHLPVVHLAQLKEGAKSPPYIFSPIPF

Parental  LGHAVAFGKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSRLTTPVFG
          LGHAVAFGKSP.EFLENAYEKYGPVFSFTMV.KTFT.LLGS.AAAL.F.SKNED.N.E.VYS.LTTP..G
Retrocopy LGHAVAFGKSPVEFLENAYEKYGPVFSFTMVSKTFTSLLGSYAAALFFTSKNEDMNVEVVYSHLTTPTCG

Parental  KGVAYDVPNP-VFLEQKKMLKSGLNIAHFRQHVSIIEKETNEYFESWGESGEKN-VFEALSELIILTAS-
          KGV.YDVPNP..F..QKK.LKSGL..A.FRQ..S.IEKET.EYFESWG...EKN..FEALSELIIL.A..
Retrocopy KGVTYDVPNP>FFFKQKKTLKSGLDLAPFRQQPSVIEKETKEYFESWGGKWEKN<LFEALSELIILMAA<

Parental  HCLHGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKNIFYKAIQKRRQSEE
          HCLHGKEIRS.LNEKV.QLYAD.DG.FSHAAWLLPGWLPLPSFR.RDRAHREIKNI.YKAIQK..Q...
Retrocopy HCLHGKEIRSHLNEKVEQLYADSDGAFSHAAWLLPGWLPLPSFRCRDRAHREIKNISYKAIQKCSQGKK

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_272 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005722	1 retrocopy	retro_amel_1512,
Homo sapiens	ENSG00000001630	2 retrocopies	retro_hsap_1248, retro_hsap_2807,
Loxodonta africana	ENSLAFG00000000066	1 retrocopy	retro_lafr_272 ,
Monodelphis domestica	ENSMODG00000010610	1 retrocopy	retro_mdom_436,
Pongo abelii	ENSPPYG00000017824	2 retrocopies	retro_pabe_1039, retro_pabe_1040,
Pan troglodytes	ENSPTRG00000019391	2 retrocopies	retro_ptro_1901, retro_ptro_859,
Tarsius syrichta	ENSTSYG00000014341	1 retrocopy	retro_tsyr_1008,