RetrogeneDB ID: retro_lafr_821

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:84952668..84953642(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000005224
• Aliases: None
• Description: None

Sequence

>retro_lafr_821
GAGCCAGAGCCGCCATGGACCTCACAGAAGAGCACCTCAGAGACCCTGCTGAAATTCTGTGCTCCGGGGCTGAGATGCAT
TATTTGGAGCAGTTTGGAAAGTCTTCCTTTAAGGAGTCTGCCTTGAGAAAACAGTCTTTATACCTTGAATTTGACCCACT
CCTGAAAGACAGCCCTAATAAATTGGTTCCCGTGGCCACCGAGGCAAACAGCATTGATGATACGCACAAGCCTTCCTCAG
GACACCTGCCTGAAGCAAAGCTGGTAGACTTTGATTTCTTAGGTGCTCTGGACGTTCCTGTGACAGACCTTCTCCCATGT
GTCCCTGGGCCTGTGGGCCTCCCTCTGCCTGCTGACCCCATGTTGAACATGCTGCAGTACAGTCAGGGGGAGCTAGATGC
GGAGGTTAAAGCCACACAAATGAAGAACCTGGAACTGAAAAGCAAGTATGAGGAGCTCCTTGTGAAATGCCTGGAGATGG
AGCAAATCATGAATGGGTTTGAAGGGACTGTAATTCAGGTGATGGAGGAGGCTCAAAAACAGAAAGAGCTTGCCAAAGCC
AAAATCCACAAGGTTCTGAAAGAAAAAGATCAACTTTTAACAGACCTGAATTCCATGAATCAATCTCTCTCTGATCATTA
TAAAACATGTGAGAAACAGGAGGAGGTGATTGAAGGATGCCGCAAGAATGAAGAATCACTGAAGGCATGTGTTGAGGACT
ACCTAACAAGAATTGAAAAGGAAGGCCGGAGATACCAAGCATTGAAGACTCACACAGAGGAGAAGTATAATCTAGCAAAG
GAGGAACTTGCTCAAATCCAGAGGCAGGCCCAAGTACAGCAGCTGAGCTTCCAGGTGAGCCTGATAAAGGAACAGATGTG
GATCCACTTGCTGGAGAAAACCCTGCAACAGCTGACTACAGAAAACAATGAACTGATCAGACTCCACAAGGACCTGATCT
CCCAGGTGGATAAA

Alignment

ORF - retro_lafr_821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.8 %
• Parental protein coverage: 51.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPTP-SLDLTKESFRDPAEVLGTGAEVDYLEQFGASSFKESALRKQSLYLKFDPLLKDSPNRLVPVATQT
          EP.P...DLT.E..RDPAE.L..GAE..YLEQFG.SSFKESALRKQSLYL.FDPLLKDSPN.LVPVAT..
Retrocopy EPEP<AMDLTEEHLRDPAEILCSGAEMHYLEQFGKSSFKESALRKQSLYLEFDPLLKDSPNKLVPVATEA

Parental  SSTQAAGTPSSGSLSEARLVEFDFLGSLDVPVPSPPACVLGPGGPPLQVGPIVDVLRYSQQDLDAAVKTL
          .S......PSSG.L.EA.LV.FDFLG.LDVPV.....CV.GP.G.PL...P....L.YSQ..LDA.VK..
Retrocopy NSIDDTHKPSSGHLPEAKLVDFDFLGALDVPVTDLLPCVPGPVGLPLPADPMLNMLQYSQGELDAEVKAT

Parental  QMENLELKSRCEELYAKNQEMGKIMDEFEGIARQVTEEAKKEKELAEAKIQKVLKERDQLTTDLNSMEKS
          QM.NLELKS..EEL..K..EM..IM..FEG...QV.EEA.K.KELA.AKI.KVLKE.DQL.TDLNSM..S
Retrocopy QMKNLELKSKYEELLVKCLEMEQIMNGFEGTVIQVMEEAQKQKELAKAKIHKVLKEKDQLLTDLNSMNQS

Parental  FSDLFKRLEKQKEVIEGYHKNEESLKKCVEDYILRIEKESQRYQALKAHAEEKLTLANEEITQVRSKAQA
          .SD..K..EKQ.EVIEG..KNEESLK.CVEDY..RIEKE..RYQALK.H.EEK..LA.EE..Q....AQ.
Retrocopy LSDHYKTCEKQEEVIEGCRKNEESLKACVEDYLTRIEKEGRRYQALKTHTEEKYNLAKEELAQIQRQAQV

Parental  EALAFQASLRKEQMRVHSLEKTIEQKTKENEELTRICDDLISKMEK
          ..L.FQ.SL.KEQM..H.LEKT..Q.T.EN.EL.R...DLIS...K
Retrocopy QQLSFQVSLIKEQMWIHLLEKTLQQLTTENNELIRLHKDLISQVDK

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_821 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000005224	1 retrocopy	retro_lafr_821 ,
Microcebus murinus	ENSMICG00000008141	1 retrocopy	retro_mmur_402,
Mustela putorius furo	ENSMPUG00000011062	1 retrocopy	retro_mputfur_117,