RetrogeneDB ID: retro_lafr_850

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:99800594..99801972(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000031914
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_lafr_850
AACTTTAGTAATGAAGAATTTGACTACCATTTCTTTGATGAAGGTTTTACTGCCAAGGACATTCTGGACCAAAAAATTAA
TGAAGTTTCTTCTTCGGATGATAAGGATGCCTTCTATGTTGCGGACCTTGGACACATCCTGAAGAAACATCTGAGGTGGT
TAAAAGCTCTTCCTCATGTCACCCCCTTTTATGCAGTCAAATGTAATGACAGCAGAGCCATAGTGAGGACTCTGGCTGCC
ATTGGAACAGGATTTGACTGTGCTAGCAAGACTGAAAAACAGTCGGTGCAGAGTCTCAGTGTGCCTCCAGAGAGAATAAT
CTATGCAAATCCTTGTAAACAAGTATCTCAAATTAAATATGCTGCCAGTAATGGAGTTCAGATGATGATTTTGATAGCGA
GGTGGAGTTGATGAAAGCTGCCAGGGCACATCCAAAGGCAAAGTTGGTTTTGCGGATTGCCACTGATGATTCCAAAGCAG
CCTGTGGTCTGAGTGTTAAATTTGGTGCCACACTCCAAACTAGCAGGCTTCTTTTAGAACGAGCTAAAGAGCTGAATGTT
GACGTCGTCGGTGTCAGCTTCCATGTGGAAAGTGGCTGTAATGACCCTGAGACCTTCGTGCAAGCCATCTCTGATGCCCG
CGGTGTCTTTGACATGGGAGATGAGGTTGGTTTCAACATGTACCTGCTGGATATTGGTCGTGGCTTTCCTGGATCTGAGG
ATGTGAAGCTTAAATTTGAAGAGATCACCAGCGTAATCAATCCAGCATTGGACAAGTATTTTCCGTCAGATTCTGGAGTG
AAAATCATAGCTGAGCCAGGCAGATACTGTGTTGCATCAGCTTTCACTCTAGCCGTTAATATCATCGCCAAGAAACTTGT
ACTAAAGGAACAGACAGGCTCTGATGATGAAGATGGATCAAGTGAACAAACCTTTAAGTACTACATGAATGATGGAGTAT
ATGGGTCATTTAATTGCATCCTTTATAATCACGCACATGTCAAGCCCCTTCTGCAAAAGAGACCCAAGCCAGATGAGAAG
TACTATTCATCTAGCATATGGGGACCGACGTGTGATGGCCTTGATCGAATTGTTGAGTGCTGTGACCTGCCAGAAATGCA
TGTGGGTGAGTGGATGCTGTTTGAAAACATGGGTCTTACACTGTTGCTGCTGCTTCTACTTTCAGTGGGTTCCAAAGACC
AACTATCTACTCCGTGATGTCTGGGCCAATGTGGCAACTCATGCAGCAAATCGAGCGCCACAACTTCTCATCTGAAGTAG
AGGAGCATGATGTCAGCACTCTGCCTGTGTCTTGTTGTGCTTGGGAAAGTGGAATGAAACACCATCCAGCAACTTGTGCT
TCAGCTAGTATTAATGTG

Alignment

ORF - retro_lafr_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.13 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NFSNEEFDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCND
          NFSNEEFD.HF.DEGFTAKDILDQKINEVSSSDDKDAFYVADLG.ILKKHLRWLKALP.VTPFYAVKCND
Retrocopy NFSNEEFDYHFFDEGFTAKDILDQKINEVSSSDDKDAFYVADLGHILKKHLRWLKALPHVTPFYAVKCND

Parental  SRAIVKTLAAIGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAASNGVQMMT-FDSEVELMK
          SRAIV.TLAAIGTGFDCASKTE.Q.VQSL.VPPERIIYANPCKQVSQIKYAASNGVQMM..FDSEVELMK
Retrocopy SRAIVRTLAAIGTGFDCASKTEKQSVQSLSVPPERIIYANPCKQVSQIKYAASNGVQMMI<FDSEVELMK

Parental  VARAHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQA
          .ARAHPKAKLVLRIATDDSKA.C.LSVKFGATL.TSRLLLERAKELN.DVVGVSFHV.SGC.DPETFVQA
Retrocopy AARAHPKAKLVLRIATDDSKAACGLSVKFGATLQTSRLLLERAKELNVDVVGVSFHVESGCNDPETFVQA

Parental  ISDARCVFDMGDEVGFNMYLLDIGGGFPGSEDVKLKFEEITSVINPALDKYFPSDSGVKIIAEPGRYYVA
          ISDAR.VFDMGDEVGFNMYLLDIG.GFPGSEDVKLKFEEITSVINPALDKYFPSDSGVKIIAEPGRY.VA
Retrocopy ISDARGVFDMGDEVGFNMYLLDIGRGFPGSEDVKLKFEEITSVINPALDKYFPSDSGVKIIAEPGRYCVA

Parental  SAFTLAVNIIAKKLVLKEQTGSDDEDESSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPKPDEKYY
          SAFTLAVNIIAKKLVLKEQTGSDDED.SSEQTF.YY.NDGVYGSFNCILY.HAHVKPLLQKRPKPDEKYY
Retrocopy SAFTLAVNIIAKKLVLKEQTGSDDEDGSSEQTFKYYMNDGVYGSFNCILYNHAHVKPLLQKRPKPDEKYY

Parental  SSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENM-GAYTVAAASTFNGFQRPTIYYVMSGPTWPLMQQI
          SSSIWGPTCDGLDRIVE.CDLPEMHVG.WMLFENM.G.YTVAAASTF.GFQRPTIY.VMSGP.W.LMQQI
Retrocopy SSSIWGPTCDGLDRIVECCDLPEMHVGEWMLFENM<GSYTVAAASTFSGFQRPTIYSVMSGPMWQLMQQI

Parental  RRHDFSRDVEEHDVGTLPVS-CAWESGMKRHPASRASASINV
          .RH.FS..VEEHDV.TLPVS.CAWESGMK.HPA..ASASINV
Retrocopy ERHNFSSEVEEHDVSTLPVSCCAWESGMKHHPATCASASINV

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_850 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,