RetrogeneDB ID: retro_lafr_567

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_216:189019..189595(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000031169
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SCO1
• Ensembl ID: ENSLAFG00000005056
• Aliases: None
• Description: None

Sequence

>retro_lafr_567
TTTGGGGCAGGGCTCGGAGGGGCCTGGCTGGCTGCTCGGGCCGAGAAGGAGCGGTGGCGGCAGCAACAGCGGACAGAGGC
CCTGCGCCAGGCGGCCGTGGGCCAGGGTGACTTTAGCCTGTTGGACCACAGGGGCCAGGCCCGCTGCAAAGCCGATTTCC
GGGGTCAGTGGGTCCTGATGTACTTTGGTTTCACCCACTGCCCTGACATCTGCCCCGATGAGCTGGAGAAGTTGGTACAG
GTGGTGCAGCAGCTGGAGGCCGACCCCAGCCTGCCACCCATGCAGCCCATCTTCGTCACTGTGGACCCAGAGCGGGACGA
TGTGCCAGCCATGGCCCGCTATGTGCAGGACTTCCATCCACGGCTGCTGGGTCTGACTGGCTCCACCGAGCAGGTAGCCC
AGGCTAGTCGCAACTACCGTGTATACTATAGTCCTGGTCCCAAGGATGAGGACCAGGACTACATCGTGGACCACTCCATT
GCCATCTACCTGCTCAACCCTGATGGTCTCTTCACCGACTACTATGGCCGGGGCAGGTCGGCCGAGCAGATCGCAGACAG
TGTGCGACGCCACATG

Alignment

ORF - retro_lafr_567 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.53 %
• Parental protein coverage: 70.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTFALGGALLAGMKYFKK-EKMEKLEKERQRSIGKPLLGGPFSLTTHTGEPKTDKDYLGQWVLIYFGFTH
          F...LGGA.LA..............E..RQ...G.....G.FSL..H.G......D..GQWVL.YFGFTH
Retrocopy FGAGLGGAWLAARAEKERWRQQQRTEALRQAAVGQ----GDFSLLDHRGQARCKADFRGQWVLMYFGFTH

Parental  CPDICPEELEKMIQVVDEIDSIPTLPNLTPLFITIDPERDTKEAIADYVKEFSPKLVGLTGTKEEIDKVA
          CPDICP.ELEK..QVV......P.LP...P.F.T.DPERD...A.A.YV..F.P.L.GLTG..E......
Retrocopy CPDICPDELEKLVQVVQQLEADPSLPPMQPIFVTVDPERDDVPAMARYVQDFHPRLLGLTGSTEQVAQAS

Parental  RAYRVYYSPGPKDEDQDYIVDHTIIMYLIGPDGEFLDYFGQNKRNAEIAGSIAAHM
          R.YRVYYSPGPKDEDQDYIVDH.I..YL..PDG.F.DY.G.......IA.S...HM
Retrocopy RNYRVYYSPGPKDEDQDYIVDHSIAIYLLNPDGLFTDYYGRGRSAEQIADSVRRHM

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_567 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000325	1 retrocopy	retro_amel_67,
Bos taurus	ENSBTAG00000021780	1 retrocopy	retro_btau_393,
Choloepus hoffmanni	ENSCHOG00000007572	7 retrocopies	retro_chof_2118, retro_chof_2547, retro_chof_2648, retro_chof_447, retro_chof_516, retro_chof_68, retro_chof_827,
Danio rerio	ENSDARG00000067593	1 retrocopy	retro_drer_14,
Equus caballus	ENSECAG00000025151	1 retrocopy	retro_ecab_50,
Erinaceus europaeus	ENSEEUG00000011060	1 retrocopy	retro_eeur_4,
Felis catus	ENSFCAG00000003959	1 retrocopy	retro_fcat_36,
Homo sapiens	ENSG00000133028	1 retrocopy	retro_hsap_1112,
Gallus gallus	ENSGALG00000013382	1 retrocopy	retro_ggal_14,
Loxodonta africana	ENSLAFG00000005056	1 retrocopy	retro_lafr_567 ,
Oreochromis niloticus	ENSONIG00000009584	1 retrocopy	retro_onil_50,
Oryzias latipes	ENSORLG00000001047	1 retrocopy	retro_olat_14,