RetrogeneDB ID: retro_lafr_83

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_29:12759093..12759585(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028761
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SKP1
• Ensembl ID: ENSLAFG00000016832
• Aliases: None
• Description: None

Sequence

>retro_lafr_83
ATGCCTTCAGTTAAGGCGCAGAGTTCTGATGGAGAGATACCTGAAGCTGATGTGGAAGTTGCCAAACAACCTGTGACTAT
CAAGACCATGGTGGAAGATTTGAGAATGGATGATGCAGGAGGTAACGACCTGGTTCCTCTACCGAATGTTAACGCAGCAA
TATTAAAACAGGTCATTCCGCGGTGCACCCACCACAAGGATGACCCTCCTCCTCCTGAGGATGATGAGAACAAAGAAAAG
AGAACAGACTGTGTCTCTGTTTGGGACCAAGAATTGCTGAAAGTTGGCCAGGGTACACTTTTTGAACTTATTCTGGCTGC
AAACTACTTAGACATGAAAGGTTTGCTTGACGTTACATGCAAGACTGTTGCTAATAGGATCAAGGGGAAAACTCCTGAGG
AGCTTCCCAAGACTTTCAATATCAAAAACGACTTTACTGAAGAGGAGGAAGCCCGGGTACGCAAAGAGAACCAGTGGTGT
GGAGAGAAGTGA

Alignment

ORF - retro_lafr_83 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPP
          MPS.K.QSSDGEI.E.DVE.AKQ.VTIKTM.EDL.MDD.G..D.VPLPNVNAAILK.VI..CTHHKDDPP
Retrocopy MPSVKAQSSDGEIPEADVEVAKQPVTIKTMVEDLRMDDAGGNDLVPLPNVNAAILKQVIPRCTHHKDDPP

Parental  PPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFN
          PPEDDENKEKRTD...VWDQE.LKV.QGTLFELILAANYLD.KGLLDVTCKTVAN.IKGKTPEE..KTFN
Retrocopy PPEDDENKEKRTDCVSVWDQELLKVGQGTLFELILAANYLDMKGLLDVTCKTVANRIKGKTPEELPKTFN

Parental  IKNDFTEEEEAQVRKENQWCEEK
          IKNDFTEEEEA.VRKENQWC.EK
Retrocopy IKNDFTEEEEARVRKENQWCGEK

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_83 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 14 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025191	5 retrocopies	retro_btau_10, retro_btau_1062, retro_btau_1253, retro_btau_1444, retro_btau_1687,
Canis familiaris	ENSCAFG00000000994	5 retrocopies	retro_cfam_1613, retro_cfam_779, retro_cfam_813, retro_cfam_889, retro_cfam_965,
Callithrix jacchus	ENSCJAG00000013613	1 retrocopy	retro_cjac_112,
Echinops telfairi	ENSETEG00000007560	5 retrocopies	retro_etel_1730, retro_etel_515, retro_etel_758, retro_etel_762, retro_etel_811,
Homo sapiens	ENSG00000113558	10 retrocopies	retro_hsap_2193, retro_hsap_2596, retro_hsap_3321, retro_hsap_3346, retro_hsap_3863, retro_hsap_4161, retro_hsap_4163, retro_hsap_4164, retro_hsap_724, retro_hsap_972,
Gorilla gorilla	ENSGGOG00000022930	7 retrocopies	retro_ggor_1288, retro_ggor_1300, retro_ggor_2601, retro_ggor_2602, retro_ggor_2796, retro_ggor_2797, retro_ggor_778,
Latimeria chalumnae	ENSLACG00000016599	1 retrocopy	retro_lcha_103,
Loxodonta africana	ENSLAFG00000016832	1 retrocopy	retro_lafr_83 ,
Microcebus murinus	ENSMICG00000017588	3 retrocopies	retro_mmur_270, retro_mmur_803, retro_mmur_997,
Myotis lucifugus	ENSMLUG00000022919	13 retrocopies	retro_mluc_1455, retro_mluc_1738, retro_mluc_1895, retro_mluc_2009, retro_mluc_2260, retro_mluc_2261, retro_mluc_2520, retro_mluc_2527, retro_mluc_2557, retro_mluc_267, retro_mluc_383, retro_mluc_841, retro_mluc_944,
Monodelphis domestica	ENSMODG00000014168	4 retrocopies	retro_mdom_1173, retro_mdom_155, retro_mdom_1648, retro_mdom_929,
Otolemur garnettii	ENSOGAG00000028707	8 retrocopies	retro_ogar_1446, retro_ogar_1510, retro_ogar_1511, retro_ogar_1890, retro_ogar_2019, retro_ogar_2728, retro_ogar_3306, retro_ogar_581,
Pongo abelii	ENSPPYG00000015783	7 retrocopies	retro_pabe_1915, retro_pabe_199, retro_pabe_2072, retro_pabe_2736, retro_pabe_2756, retro_pabe_626, retro_pabe_824,
Rattus norvegicus	ENSRNOG00000005828	6 retrocopies	retro_rnor_1391, retro_rnor_1392, retro_rnor_1465, retro_rnor_1888, retro_rnor_2166, retro_rnor_2333,