RetrogeneDB ID: retro_lafr_743

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_34:15187321..15188296(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGT1
• Ensembl ID: ENSLAFG00000012886
• Aliases: None
• Description: None

Sequence

>retro_lafr_743
AATATGGCAGTGCTGTGGTGGCTTTGGCATATACCTCTGACTGTGGTGGTGGCTCACGGGGCTCCCTCAGATCCTGCCCA
AGGGAAGAAGGTGTTAGCAGAAAAGGTCAGCCAGCTGATGGATTGGACCAAGAAAAACAGAGTGATAAGAATGAATGACA
CCATGTTCTATCATTTTGTACTAGAACCACCAAGAAACTACTCTATGATTGTGATGTTTACTGCTCTCCACGAGTTAAGA
CAGTGTGTGATGTGCAAGCATGCTGCTGAAGAATTTCATATCTTGGCAAATTCCTGGCAACATTCCAGTAAATTCACCAA
CAGGATATTTTTTGCTATGGTGGATTATGATCAAAGCCCTGAAGTCTTTCGAACGATCCAAGTGGTGTCAGTTCCAAATT
TCCTCCACTTTTCTGCGAAAAGGGAATTTACATCAGATGATATTTATCATTTGGAAGGAAGGGGTATCATAGCTGAGCAA
ATGGCTAAGTGGGTAGGTGAGAGAACAAACGTCAACATCAGAATCAGCCAGCCTACAAATGATGGTGGTCTCTTCACGTT
GGGGACGATTTTGGCGCTCACTGGCGGACTGGTGTCTTTACTGAAGAGCAAGTTTATTTTTAACAAAACTTTGTGGGCAG
TATTAGGTTTGTCTTTTGTAACTGTGATGACATCTGGTCAAATGTGGGCTCATATAAAAGGAGCATCATTTGCTCAAAGG
GACCCTCGCACGGGACATATGCATTATATCCACAGGGCGAGTTACTCTCAGTTTGTAGCAGAGACATGTATCATTGCCCT
GTTTAATATGTGCGTTTTCCTGGGAATGGTGCTGTTAGATAAAGCTGCCACATCTAGAATGAACGTTGTAAAGAGGAAGA
TGGTGTGTCTGATTGGTATCTGTCTAGTTGTAATATTCTTCAGCTGGCTGCTCTCTCTGCTTCGATTTAAACTACGTGGG
TATCCATACAGGTTT

Alignment

ORF - retro_lafr_743 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 91.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NMAARWWFWCVSATAAVALVLFYGVSSASAQRKKEMVLSEKVSQLMEWTSKRPVIRMNGDKFRRLVKAPP
          NMA..WW.W....T..VA.....G..S..AQ.KK..VL.EKVSQLM.WT.K..VIRMN...F...V..PP
Retrocopy NMAVLWWLWHIPLTVVVA----HGAPSDPAQGKK--VLAEKVSQLMDWTKKNRVIRMNDTMFYHFVLEPP

Parental  RNYSVIVMFTALQLHRQCIVCKQADEEFQILANSWRYSSAFTNKIFFAMVDFDEGSDVFQMLNMNSAPTF
          RNYS.IVMFTAL...RQC..CK.A.EEF.ILANSW..SS.FTN.IFFAMVD.D....VF......S.P.F
Retrocopy RNYSMIVMFTALHELRQCVMCKHAAEEFHILANSWQHSSKFTNRIFFAMVDYDQSPEVFRTIQVVSVPNF

Parental  INFPAKGKPKRGDTYELQVRGFSAEQIARWIADRTDVNIRVIRPPNYAGPLMLGLLLAVIGGLVYLRRSN
          ..F.AK......D.Y.L..RG..AEQ.A.W...RT.VNIR...P.N..G...LG..LA..GGLV.L..S.
Retrocopy LHFSAKREFTSDDIYHLEGRGIIAEQMAKWVGERTNVNIRISQPTNDGGLFTLGTILALTGGLVSLLKS-

Parental  MEFLFNKTGWAFAALCFVLAMTSGQMWNHIRGPPYAHKNPHTGHVNYIHGSSQAQFVAETHIVLLFNGGV
          ..F.FNKT.WA...L.FV..MTSGQMW.HI.G...A...P.TGH..YIH..S..QFVAET.I..LFN..V
Retrocopy -KFIFNKTLWAVLGLSFVTVMTSGQMWAHIKGASFAQRDPRTGHMHYIHRASYSQFVAETCIIALFNMCV

Parental  TLGMVLLCEAATSDMDIGKRKIMCMAGIGLVVLFFSWMLSIFRSKYHGYPYRY
          .LGMVLL..AATS.M...KRK..C..GI.LVV.FFSW.LS..R.K..GYPYR.
Retrocopy FLGMVLLDKAATSRMNVVKRKMVCLIGICLVVIFFSWLLSLLRFKLRGYPYRF

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_743 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000010342	1 retrocopy	retro_ggor_377,
Loxodonta africana	ENSLAFG00000012886	1 retrocopy	retro_lafr_743 ,
Oryctolagus cuniculus	ENSOCUG00000000203	1 retrocopy	retro_ocun_1807,
Pongo abelii	ENSPPYG00000020493	1 retrocopy	retro_pabe_338,