RetrogeneDB ID: retro_lafr_91

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_14:1386067..1387246(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000008485
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PDHA1
• Ensembl ID: ENSLAFG00000009426
• Aliases: None
• Description: None

Sequence

>retro_lafr_91
ATGAAGAAGATGCTCGCCGCAGTTGTCTCCCGTGTGTTGTCGGGCGTCGCCACCCAGAAGCCGTCCAGCAGAGTGCTGGT
GGCATCCTGTAACTATTCAAAACAGGCTACATTTGAAATTAAGAAATGTGATCTGTATAATTTGGAAGAGGGCCCTCCTG
TCACGGCAGAGCTCACCAGGGAGGATGGGCTCAAATACTACCGGCTGATGCAGACCGTTCGCCGAATGGAGTTAAAAGCA
GATCAGCTGTATAAGCAGAAATTCATTCGTGGTTTCTGCCATTTATGTGACGGTCAGGAAGCGTGTTGTGTTGGGCTTGA
GGCAGGTATAAGACACACGGATCATGTCATCACATCCTATCGGGCGCATGGCATATGCGTTACTCGGGGAATTCCCGTTC
GAGCAGTTCTTGCAGAGCTTACAGGACGAAGAGGAGGTTGTGCTAAAGGAAAAGGTGGATCAATGCATATGTATGCCAAG
AACTTCTACGGGGGCAACGGCATTGTTGGAGCTCAGGTGCCCCTGGGAGCTGGTATTGCCTTGGCCTGTAAATATAAGGA
AAACAAGGAGATCTGTTTGACTTTATATGGAGATGGCGCTGCTAATCAGGGTCAGCTATTTGAAGCTTACAATATGGCAG
CTTTGTGGAAATTGCCTTGTGTTTTCATCTGTGAGAATAACCGCTATGGAATGGGAACAGCTGTTGAGAGAGCAGCAGCC
ACTCCTGATTATTACAAGAGAGGCAGTTTTATTCCGGGGCTAAGGGTAGATGGAATGGATATTCTGTGTGTCCGGGAGGC
CACAAAGTTCGCCGCTGACTATTGTAGATCTGGAAAGGGGCCCATACTGATGGAGCTGCAGACTTACCGTTATCACGGAC
ACAGTATGAGTGATCCTGGAATCAGTTATCGTTCCCGGCAAGAAATTCAGGATGTAAGAAGTAAGAGTGACCCTATTATG
CTTCTCAAAGATAAAATGGTAAACAGCAAGCTTGCCACTGTGGAAGAATTCAAGGAAATTGATGGTGAAGTGAAGAAAGA
AATTGAGGATGCGGCCCAATTTGCCATAACTGATCCAGAACCACCCTTGGAGGAATTAGGCCATCACATCTACAGCAGTA
GTCCACCTTTTGAACTTCGTGGTGCAAATCAGTGGATCAAGTTTAAATCGATCAGTTAA

Alignment

ORF - retro_lafr_91 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRKMLAAV-SRVLSGAAP-KPASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLRYYRMM
          M.KMLAAV.SRVLSG.A..KP.SRVLVAS.N....ATFEIKKCDL..LEEGPPVT..LTREDGL.YYR.M
Retrocopy MKKMLAAVVSRVLSGVATQKPSSRVLVASCNYSKQATFEIKKCDLYNLEEGPPVTAELTREDGLKYYRLM

Parental  QTVRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAEL
          QTVRRMELKADQLYKQK.IRGFCHLCDGQEACCVGLEAGI..TDH.IT.YRAHG...TRG..VR..LAEL
Retrocopy QTVRRMELKADQLYKQKFIRGFCHLCDGQEACCVGLEAGIRHTDHVITSYRAHGICVTRGIPVRAVLAEL

Parental  TGRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVKEPSPFQLLTSQASTDSSCI-LYSHGPIEEYFQGQIF
          TGRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQV.......L..........C..LY..G......QGQ.F
Retrocopy TGRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYKENKEICLTLYGDGAAN---QGQLF

Parental  EAYNMAALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDVLCVREATRFAAAYCRS
          EAYNMAALWKLPC.FICENNRYGMGT.VERAAA..DYYKRG.FIPGLRVDGMD.LCVREAT.FAA.YCRS
Retrocopy EAYNMAALWKLPCVFICENNRYGMGTAVERAAATPDYYKRGSFIPGLRVDGMDILCVREATKFAADYCRS

Parental  GKGPILMELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKE
          GKGPILMELQTYRYHGHSMSDPG.SYR.R.EIQ.VRSKSDPIMLLKD.MVNS.LA.VEE.KEID.EV.KE
Retrocopy GKGPILMELQTYRYHGHSMSDPGISYRSRQEIQDVRSKSDPIMLLKDKMVNSKLATVEEFKEIDGEVKKE

Parental  IEDAAQFATADPEPPLEELGHHIYSSEPPFEVRGANQWIKFKSVS
          IEDAAQFA..DPEPPLEELGHHIYSS.PPFE.RGANQWIKFKS.S
Retrocopy IEDAAQFAITDPEPPLEELGHHIYSSSPPFELRGANQWIKFKSIS

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_91 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
Echinops telfairi	ENSETEG00000001392	1 retrocopy	retro_etel_1802,
Loxodonta africana	ENSLAFG00000009426	1 retrocopy	retro_lafr_91 ,
Macaca mulatta	ENSMMUG00000017336	1 retrocopy	retro_mmul_123,
Procavia capensis	ENSPCAG00000004196	1 retrocopy	retro_pcap_451,
Sarcophilus harrisii	ENSSHAG00000015375	1 retrocopy	retro_shar_84,