RetrogeneDB ID: retro_lafr_329

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_12:62087259..62088436(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KYNU
• Ensembl ID: ENSLAFG00000002172
• Aliases: None
• Description: Kynureninase [Source:UniProtKB/TrEMBL;Acc:G3SPY9]

Sequence

>retro_lafr_329
CACCTATTAGGAAATTCTCTTGGCCTTCAACCAAAAATGGTTAAAACATATCTGGAAGAACTAGATTTAAAAAAAAAAAA
AGGAGCCTACAGTCAAGAAGCAGGGAAATGTCCTTGGATTACAGGAGATGAGAGTATTACAGGTCTTAACAATTGACATT
GTAGGAGCCAGTGAAAAAGAAATAGCTCTAATGAATGGTTTGACTGTTAATTTACATCTTCTATGTTATCATTTTTCAAA
CCTACACCAAAATGGTATAAAATTCTTTTAGAAGCTAAAAACTCACTTTCGAATCATAACGCTATTGAGTCACAGCTTCA
ACTTCATGGACTTAATGTTGAGAAGAGTATGTGAATTATACAGCCAAGAGACGGGGAAGAAACCTTGAGAATGGAAGATA
TCCTTGAAGTAATTCAGAAGGAAGGAGAATGGATTGCAGTGATCCTCTTCAATGGGGTGCATTTTTATACTGGTCAGCTC
TTTAATATACCTGCCATCACAAAAGCTGGATGAGCAAACGGTTGTTTTATTGGCTTTGATCTAGCACATGCAGTTGGAAA
CGTCGAACCCCACTTACAGGACTGGAGAGTTGATTTTGCCTGCTGGTGTTCCTCCAAGTATTTAACTTCAGGAGCAGGAG
ATCTTGCTGGTGCCTTTGTGTAAGAAAAGCACACACATACAATAAAACCTGCATTAATGGGATGGTGTGGCCATGAACTC
AACACCAGATTTTAAATGGATAACAAACTCCAGTTAATCCCCGGGGCCAATGGATCCTGAATTTCAAATTCTTCCATTTG
TGGGTCTGTTCCTCACATGCTTAGTTTTGAGATCTTTAAACAACCAAACTATGAAAGCATTGAGGAGAAAATTTATTTTG
CTAACTGGTTATCTGGAGTACATGATCAAGCATTACTGTAACAAAAATAAAGCAGAAAGCAAGAAACCACTTGTGAACAT
AATTATTCCATCTCTTCTAGAAGATCAGGGCTGCCAGCTAACACGAACGTTGTTTGCTCCAATGAAGTATGTTTTCTGAG
ATCTAGAAGAAAGAGGAGTGGTTTGTGATAAGTAGGAACCCAATGGCGTTCTAGTGGCTTTGGTTGCTCTCTACAGTTCT
TTCCATGATGCTTATAAATTTGTCAATCTGCTCACTTCTGTACTTGACTCTGCAGAA

Alignment

ORF - retro_lafr_329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 85.06 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YFLGNSLGLQPKMVKTYLEEELDKWAKIGAYGHEVGKRPWITGDESITGL-MIDIVGANEKEIVLMNGLT
          ..LGNSLGLQPKMVKTYLEE.LD...K.GAY..E.GK.PWITGDESITGL..IDIVGA.EKEI.LMNGLT
Retrocopy HLLGNSLGLQPKMVKTYLEE-LDLKKKKGAYSQEAGKCPWITGDESITGL>TIDIVGASEKEIALMNGLT

Parental  VNLHLL-LLSFFKPTPKRYKILLEAKAFPSDHYAIESQLQLHGLNVEKSMRIIKPREGEETLRMEDILDV
          VNLHLL..LSFFKPTPK.YKILLEAK...S.H.AIESQLQLHGLNVEKSM.II.PR.GEETLRMEDIL.V
Retrocopy VNLHLL<MLSFFKPTPKWYKILLEAKNSLSNHNAIESQLQLHGLNVEKSM*IIQPRDGEETLRMEDILEV

Parental  IEKEGDSIAVILFSGVHFYTGQLFNIPAITKAGQAKGCFVGFDLAHAAGNVELHLHDWGVDFACWCSYKY
          I.KEG..IAVILF.GVHFYTGQLFNIPAITKAG.A.GCF.GFDLAHA.GNVE.HL.DW.VDFACWCS.KY
Retrocopy IQKEGEWIAVILFNGVHFYTGQLFNIPAITKAG*ANGCFIGFDLAHAVGNVEPHLQDWRVDFACWCSSKY

Parental  LNSGAGGLAGAFVHEKHAHTIKPALVGWFGHELNTRFKMDNKLQLIPGATGFRISNPPI-LLVCSLHA-S
          L.SGAG.LAGAFV.EKH.HTIKPAL.GW.GHELNTRF.MDNKLQLIPGA.G..ISN..I.L.VCS.HA.S
Retrocopy LTSGAGDLAGAFV*EKHTHTIKPALMGWCGHELNTRF*MDNKLQLIPGANGS*ISNSSI<LWVCSSHA>S

Parental  LEIFKQ-ATMQALRRKSVLLTGYLEYLIKNYHNKDKAESKKPVVNIITPPHIEERGCQLTLTFSAPMKYV
          .EIFKQ..TM.ALRRK..LLTGYLEY.IK.Y.NK.KAESKKP.VNII.P...E..GCQLT.T..APMKYV
Retrocopy FEIFKQ>QTMKALRRKFILLTGYLEYMIKHYCNKNKAESKKPLVNIIIPSLLEDQGCQLTRTLFAPMKYV

Parental  FQELEKRGVVCDKREPNGIRVAPVPLYNSFHDVYKFVSLLISVLDSTE
          F..LE.RGVVCDK.EPNG..VA.V.LY.SFHD.YKFV.LL.SVLDS.E
Retrocopy F*DLEERGVVCDK*EPNGVLVALVALYSSFHDAYKFVNLLTSVLDSAE

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_329 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013126	1 retrocopy	retro_amel_501,
Loxodonta africana	ENSLAFG00000002172	1 retrocopy	retro_lafr_329 ,
Microcebus murinus	ENSMICG00000017770	1 retrocopy	retro_mmur_940,
Mustela putorius furo	ENSMPUG00000003685	1 retrocopy	retro_mputfur_503,
Pongo abelii	ENSPPYG00000012827	1 retrocopy	retro_pabe_1439,