RetrogeneDB ID: retro_lafr_1050

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_61:11187864..11188803(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000026435
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTBP3
• Ensembl ID: ENSLAFG00000011358
• Aliases: None
• Description: None

Sequence

>retro_lafr_1050
GACATCTACAACGCCTGCTGCACGCTGCGCATCGACTTCTCCAAGCTCACCAGCCTCAATGTCAAGTACAACAACGATAA
GAGCCGTGACTACACACGTCCAGATCTGCCCTCGGGGGATAGCCAGCCGTCCCTGGACCAGACCATGGCCGCCGCCTTTG
GTGCACCTGGTATAATCTCAGCCTCTCTGTACGCAGGAGCTGGTTTTCCTCCCACCTTTGCCATTCCTCAAGCTGCAGGT
CTCTCTGTTCCCAATGTCCATGGCGCCCTGGTCCCTCTGGCCATTCCCTCGGCAGCGGCAGCGGTGGCTGCAGCAGGCCG
GATCGCCATCCCCGGCCTGGCTGGAGCAGGGAACTCTGTCCTCCTGGTCAGCAACCTCAACCCAGAGAGAGTCACACCCC
AAAGCCTCTTTATTCTTTTCGGTGTGTACGGGGACGTGCAGCGTGTGAAGGTCCTGTTCAACAAGAAGGAGAACGCTCTA
GTGCAGATGGCCGACGGAAGCCAGGCCCAGCTGGCTATGAGCCACCTCAATGGGCACAAGCTGCACGGGAAGCCCGTGCG
CATCACGCTGTCCAAGCACCAGAACGTGCAGCTGCCCCGTGAGGGCCAGGAGGACCAGGGCCTCACCAAGGACTACAGCA
ACTCGCCCTTGCATCGCTTCAAGAAACCTGGCTCCAAGAATTTCCAGAACATCTTCCCACCTTCAGCCACCCTGCATCTC
TCCAACATCCCGCCTTCGATATCCGAAGATGACCTCAAGATTCTCTTCTCAAGTAATGGAGGGATGGTCAAAGGATTCAA
GTTCTTCCAGAAGGACCGCAAGATGGCACTGATACAGATGGGCTCGGTGGAGGAGGCCATCCAGGCCCTCATTGAGCTGC
ACAACCACGACCTCGGGGAGAACCACCACCTGCGGGTCTCCTTCTCCAAGTCCACCATC

Alignment

ORF - retro_lafr_1050 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.03 %
• Parental protein coverage: 59.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NIYNACCTLRIDFSKLTSLNVKYNNDKSRDFTRLDLPTGDGQPSLEPPMAAAFGAPGIISSPYAGAAGFG
          .IYNACCTLRIDFSKLTSLNVKYNNDKSRD.TR.DLP.GD.QPSL...MAAAFGAPGIIS......AGF.
Retrocopy DIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMAAAFGAPGIISASLYAGAGFP

Parental  PAIGFPQAAGLSVSAVPGALGPLAITSS----AVTGRMTIPGAGGIPGNSVLLVTNLNPDLITPHGLFIL
          P....PQAAGLSV..V.GAL.PLAI.S.....A..GR..IPG..G..GNSVLLV.NLNP...TP..LFIL
Retrocopy PTFAIPQAAGLSVPNVHGALVPLAIPSAAAAVAAAGRIAIPGLAGA-GNSVLLVSNLNPERVTPQSLFIL

Parental  FGVYGDVHRVKIMFNKKENALVQMADANQAQLAMNHLSGQRLYGKVLRATLSKHQAVQLPREGQEDQGLT
          FGVYGDV.RVK..FNKKENALVQMAD..QAQLAM.HL.G..L.GK..R.TLSKHQ.VQLPREGQEDQGLT
Retrocopy FGVYGDVQRVKVLFNKKENALVQMADGSQAQLAMSHLNGHKLHGKPVRITLSKHQNVQLPREGQEDQGLT

Parental  KDFSNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVTVDDLKNLFTDAGCSVKAFKFFQKDRKMALIQ
          KD.SNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPS...DDLK.LF...G..VK.FKFFQKDRKMALIQ
Retrocopy KDYSNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSISEDDLKILFSSNGGMVKGFKFFQKDRKMALIQ

Parental  LGSVEEAIQALIELHNHDLGENHHLRVSFSKSTI
          .GSVEEAIQALIELHNHDLGENHHLRVSFSKSTI
Retrocopy MGSVEEAIQALIELHNHDLGENHHLRVSFSKSTI

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_1050 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002039	2 retrocopies	retro_chof_1487, retro_chof_2474,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Loxodonta africana	ENSLAFG00000011358	1 retrocopy	retro_lafr_1050 ,