RetrogeneDB ID: retro_lafr_28

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:3333423..3335373(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000011186
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000014451
• Aliases: None
• Description: None

Sequence

>retro_lafr_28
AATGAAATGGAGACTCTTCAAGAAGCAGGATTAAGGTGCCTTTCATTGGGAGAGCTTTCATGCTGGCGTATCAGGAGACA
TGTGAGCAAATTAACTAGAAGCCAAGGCTCCATGATGAATATTCAAGGAAAGAGTCCTCAATTTCCCAAGCAGCTTGATT
CCCTCTGCCAAGCAGGGGCAGGAGTTTCTGAAGATGACAAGTATATAATGAATTTTATAGGGGGTGATTCCAGTGTTATT
GAAAATCAAGAATTTCCAACTGGGAGAACTCAGAATTCTTGGAGTAAAATATATCTGAATGAGACCCAGAATTACCAGGG
AAACTGTAAGCAAACTCAAATGAAAAACAAATTATGTATATTTACTCCATGTGTTAACATTTTCAATTGCATTTCACACC
ATCATGACAATGTAGTCTACAAACGAGAGAAGACTTATAGCAACAATATTTATGGTAATGACATCTTAAAGATACCGCCT
CTTAACCAACGTAGTATAATTCTCACAGGACAGAAAACTTACCAGTGTAACGAGTGTGAAAATACTTTCAGTGATCACTT
AAGTCTTGAACTTCATCAGCAGGCACACTTGGGAAAGAAGTCCCCTACATGTAGTACACATAGAAAGGACATCAGTTATG
GCTCAGGTATTCCGTGTCAACAAAGTGTTCACACAGGGAAAAAACGCTATTGGTGTCATGAGTGTGGTAAGGGTTTTAGT
CAGAGCTCAAATCTGCAAACTCATCAGAGAGTGCACACAGGAGAGAAACCCTATACGTGCCATGAATGTGGTAAGAGTTT
TAATCAGAGCTCACATCTGTATGCTCATCTGCCTATTCACACAGGAGAGAAGCCTTACAGATGTGACAGTTGTGGGAAGG
GCTTCAGTCGTAGCACAGATCTTAATATTCATTGCAGAGTCCACACGGGAGAAAAACCTTATAAATGTGAGGTTTGTGGG
AAGGGTTTCACTCAGAGATCACATCTTCAAGCCCATCAAAGAATTCACACTGGAGAGAAACCATATAAATGTGGGGATTG
TGGTAAACGCTTTAGCTGTAGCTCAAATCTTCACACCCATCAGAGAGTCCACACTGAAGAAAAGCCATACAAATGTGACG
AATGTGGTAAGTGCTTTAGTTTGAGCTTTAATCTTCATAGTCATCAGCGGGTCCACACAGGGGAGAAACCCTATAAGTGT
GAAGAGTGTGGTAAGGGTTTTAGTTCAGCATCAAGTTTTCAGAGCCATCAGAGGGTCCACACAGGAGAGAAGCCATTTCA
ATGCAACGTGTGTGGGAAGGGCTTCAGTCAGAGTTCGTATTTTCAAGCCCATCAGAGAGTCCACACTGGAGAAAAACCAT
ACAAGTGTGAGGTGTGTGGGAAGCGCTTCAATTGGAGTTTAAATCTCCACAATCATCAAAGAGTCCACACAGGAGAGAAG
CCCTATAAATGTGAGGAATGTGGTAAGGGTTTCAGTCAGGCCTCAAATCTCCAAGCTCATCAGAGTGTCCACACTGGGGA
AAAACCATTCAAGTGTGATGCATGTCAGAAACGATTCAGCCAAGCCTCACATCTTCAAGCCCATCAGAGAGTCCACACTG
GAGAAAAACCATATAAATGTGATACATGTGGTAAGGCCTTTAGCCAGAGATCAAATCTTCAAGTGCATCAGATAATTCAC
ACTGGAGAGAAACCATTTAAGTGTGAGGAATGTGGAAAGGAATTCAGTTGGAGTGCTGGTCTCAGTGCTCATCAGAGGGT
CCACACGGGAGAGAAACCATATACATGTCAGCAGTGTGGTAAGGGCTTCAGTCAGGCCTCACATTTTCACACACATCAGA
GGGTACACACTGGAGAGAAGCCATACATATGTGATGTCTGTTGTAAGGGTTTCAGCCAGAGGTCACATCTTGTATACCAT
CAGAGAGTCCATAGTGGAGGTAATACATAG

Alignment

ORF - retro_lafr_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.21 %
• Parental protein coverage: 68.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAHQIAHRGEKPYKCEECGAGFSQSSYLRGHKRVHTTKKPYKCDECGKGFSWRSRLQAHQRIHTGEKPYK
          ..HQ.AH.G.K...C.......S..S.......VHT.KK.Y.C.ECGKGFS..S.LQ.HQR.HTGEKPY.
Retrocopy ELHQQAHLGKKSPTCSTHRKDISYGSGIPCQQSVHTGKKRYWCHECGKGFSQSSNLQTHQRVHTGEKPYT

Parental  CDACGKGFSYSSHLNIHCRIHTGEKPYKCEECGKGFSVGSHLQAHQISHTGEKPYKCEECGKGFCRLSSL
          C..CGK.F..SSHL..H..IHTGEKPY.C..CGKGFS....L..H...HTGEKPYKCE.CGKGF...S.L
Retrocopy CHECGKSFNQSSHLYAHLPIHTGEKPYRCDSCGKGFSRSTDLNIHCRVHTGEKPYKCEVCGKGFTQRSHL

Parental  HMHQRIHSGEKPFKCEECGRGFRWRDNLHSHQAVHTGEKPYKCDTCGKGFSQSSYLKVHHKIHNVEKPFK
          ..HQRIH.GEKP.KC..CG..F....NLH.HQ.VHT.EKPYKCD.CGK.FS.S..L..H...H..EKP.K
Retrocopy QAHQRIHTGEKPYKCGDCGKRFSCSSNLHTHQRVHTEEKPYKCDECGKCFSLSFNLHSHQRVHTGEKPYK

Parental  CEECGQGFHWSSRLQVHRLIHTGVKPYKCEECGKGFRQAAHLLTHQRVHSGEKPFKCEECGKYFSTRQNL
          CEECG.GF...S..Q.H...HTG.KP..C..CGKGF.Q......HQRVH.GEKP.KCE.CGK.F....NL
Retrocopy CEECGKGFSSASSFQSHQRVHTGEKPFQCNVCGKGFSQSSYFQAHQRVHTGEKPYKCEVCGKRFNWSLNL

Parental  HVHCRIHKGEKSYNCVECGKGFRQAAHLLTHQRVHSGEKPFKCEECAKYFSSRSNLKTHLRIHTGEKSYN
          H.H.R.H.GEK.Y.C.ECGKGF.QA..L..HQ.VH.GEKPFKC..C.K.FS..S.L..H.R.HTGEK.Y.
Retrocopy HNHQRVHTGEKPYKCEECGKGFSQASNLQAHQSVHTGEKPFKCDACQKRFSQASHLQAHQRVHTGEKPYK

Parental  CEECGKGFRHAANLLTHQRVHSGEKPFKCEECGKYFSSRTNLQTHGRIHTGEKSYNCEECGKGFRQAAHL
          C..CGK.F....NL..HQ..H.GEKPFKCEECGK.FS....L..H.R.HTGEK.Y.C..CGKGF.QA.H.
Retrocopy CDTCGKAFSQRSNLQVHQIIHTGEKPFKCEECGKEFSWSAGLSAHQRVHTGEKPYTCQQCGKGFSQASHF

Parental  LTHQRVHSGEKPFKCEECGKSFCQNSHLQAHQRVHN
          .THQRVH.GEKP..C..C.K.F.Q.SHL..HQRVH.
Retrocopy HTHQRVHTGEKPYICDVCCKGFSQRSHLVYHQRVHS

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_28 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000014451	1 retrocopy	retro_lafr_28 ,