RetrogeneDB ID: retro_lafr_162

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:55669664..55670455(-)
• Located in intron of: ENSLAFG00000017896

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBC1D19
• Ensembl ID: ENSLAFG00000009636
• Aliases: None
• Description: None

Sequence

>retro_lafr_162
AGTCTTCAGAGACCTGAGATTAAACTTGAATCACTAAAACAAGATCTTAAGGAGTTCTTTAAAATATCAGGTTGGGACAA
GAAACTTCAATATGCTGTTTATAGTGAATTGAGTACGTTTCCTTTACCTAGTCATCCTGTTGCCCCTCTCGAACATCTTA
AAGAACCTTCGGTATACAGGAGGAAAGCACAGGGAAGTTGGGAAAAAAGAATTCTGAAAAGTTGAAATAGTATGTTCATT
GAACTCAGTATTCTACTGGCACAAAAGAGGCCTGTTGGGGAACAGAAAGAACTTTTGAACAAATGGAATGAAATGGAAAC
TGATAAACCAGATTTAAGCCTTTTCAGACCTGTTTATGCACCTAAGGATTTTCTTGAGGTATTAATTAATCTTTGCAACC
CAAATTATGAAAACAGTGATTCTCTTAGTTTCAGGACGCATCTGCATTTAATCCAAGTTCTTCTGAAAGTAAAAGACATT
CCTGAATTGAAAGAATTCTTTGTAGAACTCAGCTTAAATACAGGACAACTGGGTCCAGATGATTCTACACAAGTGCCTCC
TGAACTTTTTGAAAATGAGCATGTACATATAGGGCAGAAGTTTTAGCAGAACAAGATAGTGCTGCTGCTCAGCAGTGTAT
CAGACAAGGAAGTCCCATAGCACTGGGAGATGAACTGTGGACTCTCATTTCAAATACTTTCAGTCAGCCTGTGGATATCT
TGTACCATGAGCAGCTGAAGACCAATGTGATACAACATGACCTTTTGGTGGACGGTCTAACAAGCAATGAT

Alignment

ORF - retro_lafr_162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 50.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLQRPEIKLESLKEDIKKFFKISGWEKKLQNAVYSELSVFPLPSHPAAPPEHLKEPLVYMRKAQGSWEKR
          SLQRPEIKLESLK.D.K.FFKISGW.KKLQ.AVYSELS.FPLPSHP.AP.EHLKEP.VY.RKAQGSWEKR
Retrocopy SLQRPEIKLESLKQDLKEFFKISGWDKKLQYAVYSELSTFPLPSHPVAPLEHLKEPSVYRRKAQGSWEKR

Parental  ILKSLNSMCTELSIPLARKRPVGEQKELLNKWNEMGTDEPDLSLFRPVYAPKDFLEVLINLRNPNYENGD
          ILKS.NSM..ELSI.LA.KRPVGEQKELLNKWNEM.TD.PDLSLFRPVYAPKDFLEVLINL.NPNYEN.D
Retrocopy ILKS*NSMFIELSILLAQKRPVGEQKELLNKWNEMETDKPDLSLFRPVYAPKDFLEVLINLCNPNYENSD

Parental  SLSFRTHLGLIQVPLKVKDIPELKESFVELSLNTGQLGIDDSTQVPPELFENEHVRIGQK-VLEEQDSAA
          SLSFRTHL.LIQV.LKVKDIPELKE.FVELSLNTGQLG.DDSTQVPPELFENEHV.IGQK.VL.EQDSAA
Retrocopy SLSFRTHLHLIQVLLKVKDIPELKEFFVELSLNTGQLGPDDSTQVPPELFENEHVHIGQK<VLAEQDSAA

Parental  AQQYIRQGSPTALRAELWTLILNISSQPEDILYYEQLKTNVIQHDLLVDSLIYKD
          AQQ.IRQGSP.AL..ELWTLI.N..SQP.DILY.EQLKTNVIQHDLLVD.L...D
Retrocopy AQQCIRQGSPIALGDELWTLISNTFSQPVDILYHEQLKTNVIQHDLLVDGLTSND

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_162 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000009636	1 retrocopy	retro_lafr_162 ,
Monodelphis domestica	ENSMODG00000000109	1 retrocopy	retro_mdom_1761,