RetrogeneDB ID: retro_lafr_312

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_12:39969135..39970022(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCTN2
• Ensembl ID: ENSLAFG00000013538
• Aliases: None
• Description: None

Sequence

>retro_lafr_312
ATGGCAGACTCTAAATACAACTTTCCTGGCATTGCCAGGAACTAGCCAGAAGCTTATGAAACCATCGGCCTACCTTAGGG
AGATCACATGGAGTTTGATGTGGAGGAGCGGAGGAGCAGAAGTGTGGAACACATCATTGTCAATCTCAACGTTGCCTATG
ACAAGTTCAAGGACAAGAAAGTGGGGATAGAGGGACTTGATTTCTCAGATTGTATTGGAAAAACCAAGGGGACAGGATAT
GAATCTAAAGAACATGAGAAGACTGGTGAAGGCCTGGGAGTAAAGGAGACAACCAGCAAAAGTACTGGTGACTACTGCAT
GAGGGCTAAGAGCTGACAACTAAAGTTGGGAAAACCAAGACAACAGTGAAGGAGTCAGCCACTGAGGAGAAATTGACCCC
TGTTGTGCTGGCTAAACAGCTGGCAGCTCCGAAGTAGCAACTGATTGTTTCCCACCTGAAAAAGCTGCTGGGACCAGATG
CTGCGATCAACCTCACTGAACAGACGGGGCTCTGGCTAAGCGCCTGCCGCTGCAGCTAGAAGCAACGAAGAACAGCAAAG
GTACTGGTTCAGGGGGAAAGACCACCAGTGGGGCCCTTCCAGAAAGCAGCTCTGACACTTACCGGTACATTCCCAGCATG
AGCAGGATGAGTTCTCTCGAGCTGCCAAAGTTGCAGAACTTGATGAATGCCTGACAAAGCTGGGGGCAACTGTATGCTAA
AATCACAATGTTAGGAGTCCCCTTTCTGCAGACCTATAGGGAACCTATCTTAAGGAGGCTGTAGAGCTGTGCAAGCAAAG
GTGAGCACCCTGGATCTTGCAGTCTTGGACCAAGTGAAGGCTCTGCTACAGAGTGTCCTGGGAAAGATGAATGAGATTGC
CAAGCAT

Alignment

ORF - retro_lafr_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.52 %
• Parental protein coverage: 73.95 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAEELTSTSVEHIIVNPNAAYDKFKDKRVGTKGLDFS
          MAD.KY...PGIARN.P..YET..LP..D..EFD.EE..S.SVEHIIVN.N.AYDKFKDK.VG..GLDFS
Retrocopy MADSKY-NFPGIARN*PEAYETIGLP*GDHMEFDVEERRSRSVEHIIVNLNVAYDKFKDKKVGIEGLDFS

Parental  DRIGKTKRTGYESGDYEMLGEGLGVKETP-QQKYQRLLHEVQELTTEVEKIKTTVKESATEEKLTPVVLA
          D.IGKTK.TGYES...E..GEGLGVKET..QQKY..LLHE..ELTT.V.K.KTTVKESATEEKLTPVVLA
Retrocopy DCIGKTKGTGYESKEHEKTGEGLGVKETT<QQKYW*LLHEG*ELTTKVGKTKTTVKESATEEKLTPVVLA

Parental  KQLAALKQQLVASHLEKLLGPDAAINLTD-PDGALAKRLLLQLEATKNTKGTGSGGKTSNGALPDSSLVT
          KQLAA.K.QL..SHL.KLLGPDAAINLT...DGALAKRL.LQLEATKN.KGTGSGGKT..GALP.SS..T
Retrocopy KQLAAPK*QLIVSHLKKLLGPDAAINLTE<TDGALAKRLPLQLEATKNSKGTGSGGKTTSGALPESSSDT

Parental  YE-LHSRPEQDKFSQAAKVAELEKRLTELEATLRCDQDTQNPLSAGLQGACLMETVEL-LQAKVSALDLA
          Y...HS..EQD.FS.AAKVAEL...LT.L.AT.........PLSA.L.G..L.E.VEL..QAKVS.LDLA
Retrocopy YR<VHSQHEQDEFSRAAKVAELDECLTKLGATVC*NHNVRSPLSADL*GTYLKEAVEL<VQAKVSTLDLA

Parental  VLDQVEARLQSVLGKVNEIAKH
          VLDQV.A.LQSVLGK.NEIAKH
Retrocopy VLDQVKALLQSVLGKMNEIAKH

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_312 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000233	3 retrocopies	retro_cfam_1095, retro_cfam_385, retro_cfam_579,
Dipodomys ordii	ENSDORG00000007137	1 retrocopy	retro_dord_441,
Loxodonta africana	ENSLAFG00000013538	1 retrocopy	retro_lafr_312 ,
Mustela putorius furo	ENSMPUG00000001840	1 retrocopy	retro_mputfur_197,
Procavia capensis	ENSPCAG00000016236	1 retrocopy	retro_pcap_430,