RetrogeneDB ID: retro_lafr_506

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:52845623..52846552(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000000631
• Aliases: None
• Description: None

Sequence

>retro_lafr_506
CTGTACAGCAACAGAGCAGAGTGGGCAGATAAAGATCCAATGCCAAAGAGCGATGGCCCCAATCCACTGGCTCAGATCAT
TTATAGTGAAAAATTTGGAGATGTTTATGATTATTTCCCGGCTGTGGCTGCAGCCTGATGAAAAGAGTGAACAGTCTTTT
AAACTAATATGAGATGTTATTGAGTTAAATGCAGCCAATAATGCATTTTCGGAGAGTTCTCTTAAAGTCATTTCAAAAGG
ATCTTCACAGGAGGAAACGAACTATATCACTGCAATAATTAAGGAACAGCCCCCAACCTATCAAGCTTAGCATCCTAGGC
GAGCCTTAGTGGAACGGCTGAAAGATCTATCTCAGGAGCTGATAATTACTGCTGATATTCTTAATCAGGATGCAAAGAAA
TACCATGCCTGGCAGTGTGGACAGTGAATTACTCAGGAATTAAAATGTTGGGATAACGAACTGCAATATGTAGACCAACT
TCTCAAAGAAGCTGTGAGAAATAACTCTGTCTGGAATCAAAGGTACTTTGTAATTTCTAACACCACTGGCTACAGTAATC
CTGCTGTATTGAAGAGAGAAGCCTAGTATAGTCTGGAAATGATCAAACTAGTACCACATAGTGAAAGTGCATGGAACTTC
TTGAGAAGGATTTTGCAGGATTGTGGCCTTTTGAAATATTCCAATCTGTTCAATCAATTGCTTGATTTACAACCAAGTCA
CAGTCTTCCCTACCTAATTGCCTTTCTTGTGGATATCTATGAAGACAGACTAGAAAACCAATATGACAACAAGGAGGACA
TTCTTAAAGCATTAGAGTTGTGTGACATCCCAGCTAAAAAAAAAGGACAGTAGAGGAAAGGAATATCAGAGATATATTGG
ACAATCACTTGAAAGCAAACACAGCACAGAAAGTCACTGACCAACCAGT

Alignment

ORF - retro_lafr_506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.16 %
• Parental protein coverage: 99.68 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IFRDRAEWADVDPVPQNDGPNPVVQIIYSEKFRDVYDYFRAV-LQRDERSERAFILTRDAIELNAANYTV
          ....RAEWAD.DP.P..DGPNP..QIIYSEKF.DVYDYF.AV.LQ.DE.SE..F.L..D.IELNAAN...
Retrocopy LYSNRAEWADKDPMPKSDGPNPLAQIIYSEKFGDVYDYFPAV>LQPDEKSEQSFKLI*DVIELNAANNA-

Parental  WHFRRVLLKSLQK-DLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHA
          ..F....LK...K....EE.NYITAII.EQP..YQ..H.RR.LVE.LKD.SQEL...ADILNQDAK.YHA
Retrocopy --FSESSLKVISKGSSQEETNYITAIIKEQPPTYQA*HPRRALVERLKDLSQELIITADILNQDAKKYHA

Parental  WQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDPVLLEREVQYTLEMIKLVPH
          WQ..Q...QE.K.WDNELQYVDQLLKE.VRNNSVWNQRYFVISNTTGY..P..L.RE..Y.LEMIKLVPH
Retrocopy WQCGQ*ITQELKCWDNELQYVDQLLKEAVRNNSVWNQRYFVISNTTGYSNPAVLKREA*YSLEMIKLVPH

Parental  NESAWNYLKGILQDRGLSRYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCE
          .ESAWN.L..ILQD.GL..Y.NL.NQLLDLQPSHS.PYLIAFLVDIYED.LENQ.DNKEDIL.KALELC.
Retrocopy SESAWNFLRRILQDCGLLKYSNLFNQLLDLQPSHSLPYLIAFLVDIYEDRLENQYDNKEDIL-KALELCD

Parental  ILA-KEKDTIRKEYWRYIGRSLQSKHSTESDRPAN
          I.A.K.KD...KEY.RYIG.SL.SKHSTES..P..
Retrocopy IPA>KKKDSRGKEYQRYIGQSLESKHSTESH*PTS

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_506 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008272	1 retrocopy	retro_eeur_532,
Homo sapiens	ENSG00000168522	1 retrocopy	retro_hsap_805,
Loxodonta africana	ENSLAFG00000000631	1 retrocopy	retro_lafr_506 ,
Monodelphis domestica	ENSMODG00000010003	1 retrocopy	retro_mdom_1656,
Nomascus leucogenys	ENSNLEG00000012979	1 retrocopy	retro_nleu_2408,
Sorex araneus	ENSSARG00000009660	1 retrocopy	retro_sara_109,
Ictidomys tridecemlineatus	ENSSTOG00000011626	1 retrocopy	retro_itri_1221,