RetrogeneDB ID: retro_lafr_218

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:102362494..102363299(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ODC1
• Ensembl ID: ENSLAFG00000005330
• Aliases: None
• Description: None

Sequence

>retro_lafr_218
GCCGCACTCAGAACCAGCAAGCTTCCTTTGGAATGGGCTGAAGAGCTAAATATTGATATCATTGGTGTCAGCTTCCATGT
GGGAAGTGGCTGTACCGACCCTGAGACCTTTGTGCTGGCCATCTCTGATAACCGCTGTGTCTTTGACATGGGAGCTGAGG
TTGGTTTCAGCATGTGTCTGCTTGATATTGGTGGCGGCTTTCCTGGATCTGAGGATGTGACGCTTAAATTTGAAGAGATC
ACCAGTGTAATCAACCCAGCAATTGACAAGTATTTTCCATCAGATTCTGGAGTGAAAATCATAGTTGAGCCAGGCAGATC
CTATGTTGCATCAGCTTTCACCCTTGGTGTTAATATTGTAAAGAAAATTGTATGAAAGAAACAGATAGGCTCTGATAAAG
CTGAATCAAGTGAACAAACCTTTATGTATTATGTGAATGATGGAGTTTATGGATCAGTTCAACTGCGTCCTTTATGATCA
CGCACATGTAAAGCCCCTTCTGCAAAAGTGCCCCAAGCCAGATGAGAAGTATTATTCATCTAGCATGTGGGGACTGACAT
GTGATGGCCTTGATTGGATTGTTGAACACTGTGACCTGCTAGAAATGCATGTGGGTGATTAAATGCTGTTCGAAAAGTTC
GGTGCTTACACTGTTGCTGCTGCTTCTACTTTCGATGGGTTCCAGAGGCCAGCTATCTGCTATGTGATGTCCAGGCCAAC
ATGGCAACTCATGCAGCAAATCGAGAGCCACGACTTCCCATCTGAAGTGGAGGAGCAGGATGTCAGCACGCTGCCTGCCC
TGTGC

Alignment

ORF - retro_lafr_218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.81 %
• Parental protein coverage: 58.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ATLKTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGDEVGFNMYLLDIGGGFPGS
          A.L.TS.L.LE.A.ELNID..GVSFHVGSGCTDPETFV.AISD.RCVFDMG.EVGF.M.LLDIGGGFPGS
Retrocopy AALRTSKLPLEWAEELNIDIIGVSFHVGSGCTDPETFVLAISDNRCVFDMGAEVGFSMCLLDIGGGFPGS

Parental  EDVKLKFEEITSVINPALDKYFPSDSGVKIIAEPGRYYVASAFTLAVNIIAKKLVLKEQTGSDDEDESSE
          EDV.LKFEEITSVINPA.DKYFPSDSGVKII.EPGR.YVASAFTL.VNI..KK.V.K.Q.GS.D..ESSE
Retrocopy EDVTLKFEEITSVINPAIDKYFPSDSGVKIIVEPGRSYVASAFTLGVNIV-KKIV*KKQIGS-DKAESSE

Parental  QTFMYYVNDGVYGS-FNCILYDHAHVKPLLQKRPKPDEKYYSSSIWGPTCDGLDRIVERCDLPEMHVGDW
          QTFMYYVNDGVYGS.FNC.LYDHAHVKPLLQK.PKPDEKYYSSS.WG.TCDGLD.IVE.CDL.EMHVGD.
Retrocopy QTFMYYVNDGVYGS>FNCVLYDHAHVKPLLQKCPKPDEKYYSSSMWGLTCDGLDWIVEHCDLLEMHVGD*

Parental  MLFENMGAYTVAAASTFNGFQRPTIYYVMSGPTWPLMQQIRRHDFSRDVEEHDVGTLPVSC
          MLFE..GAYTVAAASTF.GFQRP.I.YVMS.PTW.LMQQI..HDF...VEE.DV.TLP..C
Retrocopy MLFEKFGAYTVAAASTFDGFQRPAICYVMSRPTWQLMQQIESHDFPSEVEEQDVSTLPALC

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_218 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 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Choloepus hoffmanni	ENSCHOG00000010898	2 retrocopies	retro_chof_1618, retro_chof_2111,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Equus caballus	ENSECAG00000022690	2 retrocopies	retro_ecab_1002, retro_ecab_957,
Loxodonta africana	ENSLAFG00000005330	2 retrocopies	retro_lafr_218 , retro_lafr_850,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Mustela putorius furo	ENSMPUG00000013321	1 retrocopy	retro_mputfur_1272,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,
Tursiops truncatus	ENSTTRG00000004611	3 retrocopies	retro_ttru_1940, retro_ttru_731, retro_ttru_843,