RetrogeneDB ID: retro_lafr_976

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_55:9719487..9719863(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028150
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MGST1
• Ensembl ID: ENSLAFG00000002693
• Aliases: None
• Description: None

Sequence

>retro_lafr_976
ATGGTTGACCTCATCCAACTAATGGAGAATGAAGTATTCACGGCCTTTGTCTCCTTTACAACAAACATTCTTTCAAAACT
GATGTTTGTGAGTACTGCAACTGCACTCTATAGGTCAGCAAGAAAGGTTTTTGTCAACCCAGAAGACTGTGCACAGTACG
GCAAAGGCAAAAATGCCAAACGGTATCTTTGGACACACGGCGTGGTGGAACATATACAAAGACCCACCTGAATGACCTTG
AAAATATCATGCCATTTCTTGGCATTCGCCTTCTGTATTCCTTGAGTGATCCAGATGTCTCAACAGCCCTCCAGCACTTC
AGACTCTTTGCTGGAGCACAGATATCCACACAACTGCATATTTGACACCCCTTCCC

Alignment

ORF - retro_lafr_976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.53 %
• Parental protein coverage: 81.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVDLTQVAENEAFMAFASYATIILSKMMFMSTATAFQRLTKKVFVNPEDCAHFGKGENAKKYLRTDDRVE
          MVDL.Q..ENE.F.AF.S..T.ILSK.MF.STATA..R...KVFVNPEDCA..GKG.NAK.YL.T...VE
Retrocopy MVDLIQLMENEVFTAFVSFTTNILSKLMFVSTATALYRSARKVFVNPEDCAQYGKGKNAKRYLWTHGVVE

Parental  RVRR-AHLNDLENIVPFLGIGLLYSLSGPDVSTALLHFRLFVGSRI-YHTIAYLTPLP
          ...R..HLNDLENI.PFLGI.LLYSLS.PDVSTAL.HFRLF.G..I..HT.AYLTPLP
Retrocopy HIQR<THLNDLENIMPFLGIRLLYSLSDPDVSTALQHFRLFAGAQI<IHTTAYLTPLP

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_976 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 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013004	3 retrocopies	retro_chof_1564, retro_chof_1842, retro_chof_2298,
Callithrix jacchus	ENSCJAG00000021590	1 retrocopy	retro_cjac_745,
Echinops telfairi	ENSETEG00000007466	7 retrocopies	retro_etel_142, retro_etel_1541, retro_etel_1615, retro_etel_1727, retro_etel_2045, retro_etel_789, retro_etel_989,
Loxodonta africana	ENSLAFG00000002693	1 retrocopy	retro_lafr_976 ,
Myotis lucifugus	ENSMLUG00000002358	1 retrocopy	retro_mluc_1078,
Tupaia belangeri	ENSTBEG00000016248	6 retrocopies	retro_tbel_1229, retro_tbel_2494, retro_tbel_3452, retro_tbel_3654, retro_tbel_366, retro_tbel_4500,