RetrogeneDB ID: retro_lafr_708

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_31:26599928..26601142(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000028514
• Aliases: None
• Description: None

Sequence

>retro_lafr_708
GAACCTTATTCAGCCCAGCAGGAGGCACCAGCTCAGTCTCCTGAGCGCCCTGAGGTGGTAGAATCTTCTCCGGTCCTACA
GGAGACTCCACCTCAGCCTCTAGAGTCTACTACACAGGTGGAAACTTCCCCACAGCAGCACGAGATCCCATTTCAGAGTC
CAGAGCCCCCCAAGGAGTTTGAACCTTCTCCAGTCCAGCAGGAGGCTCCGGCTCAGTCTCCCGAGCCACCTACCCAAGTT
AAACCTCCATCCCAGGAGGAGGCCCCAGCTCTTACACGAGAACCCACTAAGGAAGTAGAATCTTCTCTGGTCCAGCAGGA
GACTCCGTCTCAGCGTCCAGAGTCTCTTACACAGGTGGAAACTTTCCCCCAAAAGCAAGGAATCCCGTTTCAGACTCCAG
AGCCCCCAAAGGAGGTTGAACATTCGCCAGCCCAGCAGGAGGCTCCAGCTCAGCCTGCAAAGCCCTCTGATGAGGATGAA
CCTTCTCCAGGCCTGCAGGAAACCCCATCTCAGCCTCCAAATCCTCCAGAGAAAGTTAAATGTTGTCCAGTCCGGGGGGA
AGTCCCAGCTCAGCCTCCAAAACCCTCTGAGGAGGTTGAAGCTTCTCCACGCAGGAGGAAGGCCCAGCACAGCCTCCAGA
GCCCTCTGAGGAGGTGGAAGATTGTCCAGTCCCGCAAGACGCTCCAGCTCATCCTCCAGTGCCCTCTGAGGAGGCTGAAT
CTTCTCCAGTCCAGCAGGAGGCTCCAGCTCTGCCTCCAAAACTCTCTCAGGAGGTTGAACTTTCTCCAACCCATCAGGAA
GCCCCAGCACAGCCTCCAAAGCCCTCTGAGGCGGTTGAATCTTCTCAACTCCAGCAGAAAATCCCAGCACAGCCTCCAAA
GCCCTCTGAGGAGGTTGAAGCCTCTCCATTGCCACAGGAGGCTCCAGCTCGGCCTCCGAAGCCCTCTTAGGAGGTTGAAC
CTTCTTCAATCCAGCAGGAATTCCCAGTTCAGCCTCCAAAGCAGTCTGAGGCACATAAACCTTCTCCACTCCTGGAGGAA
TCCCAGGTGCAGCCTCCAAAGCCCTCTGAGGAGATCAAACCTTATCCAGTCCAGCAGGAAGCACCAGCTCAGCCTCTAAA
GCCCTCTGAGTAAGTTGAACCTCCTCCAGTCCAACAGCATTTCCCAGGTCCACCTCCAGAGCGTCCTGAGGAGGTTGAAC
CTTCTCCAGTTCAG

Alignment

ORF - retro_lafr_708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.58 %
• Parental protein coverage: 97.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KPYLAHQEAPHLPLEPPTEMEPSRLQQEAPAETLQTTEGVKP-PVQQEAPSQPPELHHEVSLQTPGRNQP
          .PY.A.QEAP....E.P...E.S...QE.P...L..T..V...P.Q.E.P.Q.PE...E..........P
Retrocopy EPYSAQQEAPAQSPERPEVVESSPVLQETPPQPLESTTQVETSPQQHEIPFQSPEPPKEFEPSPVQQEAP

Parental  HHSTLPNITMQPVDVELT--LTPEHKKEVQSCPTQQEAPAQPPKPPQEEVEPSPIQQEAPAQPPERPEEV
          ..S..P.....P...E....LT.E..KEV.S...QQE.P.Q.P......VE..P..Q..P.Q.PE.P.EV
Retrocopy AQSPEPPTQVKPPSQEEAPALTREPTKEVESSLVQQETPSQRPES-LTQVETFPQKQGIPFQTPEPPKEV

Parental  EPSSVQQEAPAQPPKPSEGVKPSPGMQEAPAQPPTPLEEVKPSPVQAEAPAKPPKLSEEVEHSPGH-EEA
          E.S..QQEAPAQP.KPS....PSPG.QE.P.QPP.P.E.VK..PV..E.PA.PPK.SEEVE.SP...EE.
Retrocopy EHSPAQQEAPAQPAKPSDEDEPSPGLQETPSQPPNPPEKVKCCPVRGEVPAQPPKPSEEVEASPRR<EEG

Parental  PAQPPKPPEEVEASPVSQEAPLHPPKPSEEGEPSPVPQEVPVQPPKPSEEVEPSPVQQEAPALPPKPLEE
          PAQPP.P.EEVE..PV.Q.AP.HPP.PSEE.E.SPV.QE.P..PPK.S.EVE.SP..QEAPA.PPKP.E.
Retrocopy PAQPPEPSEEVEDCPVPQDAPAHPPVPSEEAESSPVQQEAPALPPKLSQEVELSPTHQEAPAQPPKPSEA

Parental  SPALPPEPSQEVEPSPMQQEAIAQSLNPPQKLEAPAQPPKPSEEVEPPPAQEEAPAQPPKPLEEVESSPV
          .............P.....E..A..L..PQ..EAPA.PPKPS.EVEP...Q.E.P.QPPK..E....SP.
Retrocopy VESSQLQQKIPAQPPKPSEEVEASPL--PQ--EAPARPPKPS*EVEPSSIQQEFPVQPPKQSEAHKPSPL

Parental  QLEAPAQPPKPSEEVELPPVQQEAPAQPPKPSEEVELPPVQQEAPAQLLKPHHEVKPSPSQ
          ..E...QPPKPSEE....PVQQEAPAQP.KPSE.VE.PPVQQ..P........EV.PSP.Q
Retrocopy LEESQVQPPKPSEEIKPYPVQQEAPAQPLKPSE*VEPPPVQQHFPGPPPERPEEVEPSPVQ

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_708 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	ENSLAFG00000028514	1 retrocopy	retro_lafr_708 ,
Pongo abelii	ENSPPYG00000008498	1 retrocopy	retro_pabe_1517,