RetrogeneDB ID: retro_lafr_1156

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_798:20860..21610(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000011431
• Aliases: None
• Description: None

Sequence

>retro_lafr_1156
AATGGGACCTGTCAAACTACCTTCAAGACTGGTGTGTTTATCCTTGGTGTTCCTGTCCAGCCTGTGGTTTTAGGATACAC
AAATAAGCTGGACACGATCATGTGGACGTGGCAAGGACCTGGAGTGCTGGAAATGCTGTGGCTCGCCCTGTGTCAGTTTC
ACAGTTAGGTGGAAATTGAGTTTCTCCCAGTTTACCACCCTTCCAAGGCGAAGAGGAGCCCGGTGCTATACGCCAGCAGC
ATGAGGCGCGTCATGGCAGAGACCCTGGGCGTCTCCATCATGGATTTCACGTTTGAGGATCGTTAGCTGGCCCCAGCGGA
AGGACAGTCCGTCTCCCCTCCGACACTTGCCTTCTAGAATTCGCCAGGCTTGTGAGAGGCCTGGGGCTAAAGCTAGAAAA
ACTTTGAAAAAGATCAGAAAGCGCAAGGTGAAGAAGGGCGAGAAGACTGACTTGTGGAGTTCACGGAGTACTTGGAGGTA
CCCCTTTCCGACACGCTGGACTGCATGTTCTCACTGTTTGACGAGAGCGGAGGTGGCAAGATGGACCTGCGGGAATATGT
GATCGCCTTGTCCGTGGTCTGCAGAGCGTCTGAGACTCTGGACACCATCCAGCTGCCATTCAAGAGGTATGCATGGCATA
AGGACGGCTGCATAAATGAGGAAGACCTGTCCTGCATTCTGAAGACGGCCTTGGGCGTGACAGAGCTGCTTCTGATACAC
CTCTTCAGCGGTGTGGATGAAGATGAGAAG

Alignment

ORF - retro_lafr_1156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.36 %
• Parental protein coverage: 53.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NGVCAVPFFSGAFIPGVPVQPVVLRYPNKLDTITWTWQGPRALEILWLTLCQFHNQVEIEFLPVYHPSEE
          NG.C...F..G.FI.GVPVQPVVL.Y.NKLDTI.WTWQGP..LE.LWL.LCQFH..VEIEFLPVYHPS..
Retrocopy NGTCQTTFKTGVFILGVPVQPVVLGYTNKLDTIMWTWQGPGVLEMLWLALCQFHS*VEIEFLPVYHPSKA

Parental  EKRNPALYASNVRRVMAEALGVSITDYTFEDCQLALAEGQ-LRLPSDTCLLEFARLVRGLGLKPEKLEKD
          .KR.P.LYAS..RRVMAE.LGVSI.D.TFED..LA.AEGQ..RLPSDTCLLEFARLVRGLGL...KLEK.
Retrocopy -KRSPVLYASSMRRVMAETLGVSIMDFTFEDR*LAPAEGQ<VRLPSDTCLLEFARLVRGLGL---KLEK-

Parental  LDKYAENT-KLKKGEKIDL-LEFAAYLEVPVSDTLEGMFSLFDESGSGKMDLREYVVALSVVCRPSKTLD
          L.K..E...K.KKGEK.DL..EF..YLEVP.SDTL..MFSLFDESG.GKMDLREYV.ALSVVCR.S.TLD
Retrocopy L*KRSESA<KVKKGEKTDL<VEFTEYLEVPLSDTLDCMFSLFDESGGGKMDLREYVIALSVVCRASETLD

Parental  TIQLAFKMYASPDDGCISEEDLSCILKTALGVAELPVTDLFSAIDEDRK
          TIQL.FK.YA...DGCI.EEDLSCILKTALGV.EL....LFS..DED.K
Retrocopy TIQLPFKRYAWHKDGCINEEDLSCILKTALGVTELLLIHLFSGVDEDEK

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_1156 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000003965	1 retrocopy	retro_lafr_66,
Loxodonta africana	ENSLAFG00000011431	1 retrocopy	retro_lafr_1156 ,