RetrogeneDB ID: retro_lafr_521

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:570044..570689(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIB
• Ensembl ID: ENSLAFG00000018698
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:G3TLB6]

Sequence

>retro_lafr_521
ATACTGCACCTGCCAGGGTGGAATACAAACCTGCTCTTCGCCTCCGCCCTCATTGTGGGCTCGGTCTCCCTCCTGATGCT
CCCAGGGCCCTCTGTGGCTGATGAAAAGAAGGGCCCCAAAGTCACCATCAAGGTGCACTTGGACCTGTGAATTTAAGATG
AAGATGTAGGCCAGATGGTCATCAGTCTCTTCGGAAAGACTATTGCAAAAACAGTGGATCATTTTGTGACCTTAGCTATA
AGACACAAAGTGTTTTGCTATAAGGACAGCAAATTCCATTGTATGATCTAGGACTTCATAATCCAGGGCGGAGGCTTCAC
CCTAGGAGATGGCGCTGCAGGAAAGAGCATCTATGGCGAACGCTTCCCCAATGAGAACTTCAAGCTGAAACACTATGGGC
CCACCTGGGTGAGCATGACCAATGTAGGCAAAGACAACAATGGCTCCCAATTCTTTCTCACTACAGTTAAGACACCCTGG
TTAGATGGCAAGCATATGGTGTTTTGCAAAGTTCTAGAAGGCATGGATGCAGTACGGAAGGTGGAGAGCACCAAGATAGA
TGCTTGGGACAAGCCCCTAAAGGATGTGACAATTTCAGACTACAGCAAGATCAAGGTGAAGAAGCCCTTTGCCATCACCA
ATGAG

Alignment

ORF - retro_lafr_521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRLSERNMKLLFAAALIVGSVFFLLLPGPSVADEKKKGPKVTVKVYFDLRIGDEDVGRVVIGLFGKTVP
          .L.L...N..LLFA.ALIVGSV..L.LPGPSVADEKK.GPKVT.KV..DL.I.DEDVG..VI.LFGKT..
Retrocopy ILHLPGWNTNLLFASALIVGSVSLLMLPGPSVADEKK-GPKVTIKVHLDL*I*DEDVGQMVISLFGKTIA

Parental  KTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGERFPDENFKLKHYGPGWVSM
          KTVD.FV.LA...K.F.YKDSKFH..I.DF.IQGG.FT.GDG..GKSIYGERFP.ENFKLKHYGP.WVSM
Retrocopy KTVDHFVTLAIRHKVFCYKDSKFHCMI*DFIIQGGGFTLGDGAAGKSIYGERFPNENFKLKHYGPTWVSM

Parental  ANAGKDTNGSQFFITTVKTSWLDGKHVVFGKVLEGMDVVRKVESTKTDSRDKPLKDVTIADCGKIEVEKP
          .N.GKD.NGSQFF.TTVKT.WLDGKH.VF.KVLEGMD.VRKVESTK.D..DKPLKDVTI.D..KI.V.KP
Retrocopy TNVGKDNNGSQFFLTTVKTPWLDGKHMVFCKVLEGMDAVRKVESTKIDAWDKPLKDVTISDYSKIKVKKP

Parental  FAIAKE
          FAI..E
Retrocopy FAITNE

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_521 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017053	1 retrocopy	retro_cfam_1999,
Equus caballus	ENSECAG00000017164	1 retrocopy	retro_ecab_617,
Echinops telfairi	ENSETEG00000012671	1 retrocopy	retro_etel_1493,
Loxodonta africana	ENSLAFG00000016750	1 retrocopy	retro_lafr_469,
Loxodonta africana	ENSLAFG00000018698	1 retrocopy	retro_lafr_521 ,
Loxodonta africana	ENSLAFG00000028161	2 retrocopies	retro_lafr_1187, retro_lafr_435,
Oryctolagus cuniculus	ENSOCUG00000012012	1 retrocopy	retro_ocun_413,