RetrogeneDB ID: retro_lafr_1193

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_86:4542635..4543570(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ST6GALNAC2
• Ensembl ID: ENSLAFG00000021338
• Aliases: None
• Description: None

Sequence

>retro_lafr_1193
AAGGCCCAGGCCTGCCCCCGGCCCCTGGCCCTGGCCCTGCAGCGGTGCTCGCGCTTCTAGCGGCTCTTCGACGTCTCCAC
CCCGGTACTCCTGTGGCGCGGCCTCCTCACACAGGAGCTCTGGGACCACCTGAGCCAGCACAGACCTCCTTACGGCTGGC
AGGGCCTTTCCCGCCACACCATCGCTTCCACCCTGAGCCTGCTGAATGGCTCCGAGAGCGCGAAGCTGCTGGCCACCTCC
ACGGGGCCGCGTCCAGACTGCGCTCGCTGTGCCGTGGTGGGCAACGGAGGCACCCTGAACGGCTCTGGCCAGGGCCGCCA
CATCGACGCCCACGACTACGTTTTCAGCCTCAATGGCGCTGTGATCAAAGGTTTCGAGGCCGATGTAGGCACCAAGACCT
CCTTCTACGGTTTCACTGTGAACAGTATGAAGAACTCCCTTATCAACTACCAGGGCTTGGGCTTCACCTCCGTGCCCCAA
GGACAGGACCTGCGCTATATCTTCATCCCTCACAAAGCCGCGACTACAGGATGCTGAGGTCGGCCATTCTGGGTGTGCCT
GTCCCCGAGGGCCTTGACAAAGGAGACAATCCTCAGACCTATTTTGGGCCAGAGGCCTTTGCCGGCAAATTCCAACTACT
ACATCCGACCTTCATCCACTACCTGAGAGAGAGGTTTTTAAAATCCAAATTGATCAACACGGATGCTGGGGACTATTACG
TGCCTAGTACTGGGGCCCTCATGCTGCTGACGGCTTTGCATACCTGTGACCAGGTTAGTGCCTATGGATTCATCACCAGC
AAATACTGGAAATTTCCTGAGCACTATTTCGATAGATGGAAGACACCACTGAGATTTTACACAAACCATGATTTGAGGCT
TGAGGCCAGTCTGTGGAGGACCTTGCACAAGGCCAACATCATTGATCTGTACCAG

Alignment

ORF - retro_lafr_1193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.12 %
• Parental protein coverage: 83.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSRLCRCPLHFAIQRHPHFRRLFNLSTPVLLWGRPFTQELWDSLSQHKAPYGWQGLSHQAIASTLNLLNG
          K...C..PL..A.QR...F.RLF..STPVLLW....TQELWD.LSQH..PYGWQGLS...IASTL.LLNG
Retrocopy KAQACPRPLALALQRCSRF*RLFDVSTPVLLWRGLLTQELWDHLSQHRPPYGWQGLSRHTIASTLSLLNG

Parental  SENAELFAASKELRPDCIRCAVVGNGGILNGSRQGPNIDAHDYVFRLNGAVIKDFEDDVGTRTSFYGFTV
          SE.A.L.A.S...RPDC.RCAVVGNGG.LNGS.QG..IDAHDYVF.LNGAVIK.FE.DVGT.TSFYGFTV
Retrocopy SESAKLLATSTGPRPDCARCAVVGNGGTLNGSGQGRHIDAHDYVFSLNGAVIKGFEADVGTKTSFYGFTV

Parental  NTMKNSLISYRKLGFTSVPQRQDLHYIFI-PSDIRDYVMLRSAILGVPVPEGTDKGDKPQTYFGPEASAS
          N.MKNSLI.Y..LGFTSVPQ.QDL.YIFI.PS..RDY.MLRSAILGVPVPEG.DKGD.PQTYFGPEA.A.
Retrocopy NSMKNSLINYQGLGFTSVPQGQDLRYIFI<PSQSRDYRMLRSAILGVPVPEGLDKGDNPQTYFGPEAFAG

Parental  KFKLLHPDFIRYLTERFLKSELMNTNFRDLYMPSTGALMLLTALHTCDQVSAYGFITRNYRKFSDHYFDR
          KF.LLHP.FI.YL.ERFLKS.L.NT...D.Y.PSTGALMLLTALHTCDQVSAYGFIT..Y.KF..HYFDR
Retrocopy KFQLLHPTFIHYLRERFLKSKLINTDAGDYYVPSTGALMLLTALHTCDQVSAYGFITSKYWKFPEHYFDR

Parental  IKKPLIFYANHDLHLEAALWGDLHKAGIIWLYQ
          .K.PL.FY.NHDL.LEA.LW..LHKA.II.LYQ
Retrocopy WKTPLRFYTNHDLRLEASLWRTLHKANIIDLYQ

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_1193 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	ENSLAFG00000021338	1 retrocopy	retro_lafr_1193 ,