RetrogeneDB ID: retro_lafr_505

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:48363641..48364101(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MESDC2
• Ensembl ID: ENSLAFG00000014513
• Aliases: None
• Description: None

Sequence

>retro_lafr_505
ATGGCGGTCTCCAGCTGGGCAGGCGTGGCCGTGCTCCTGCTTTCTCTTCTGACCTTCTGTTACTGAGGCTGCTACCACCT
TGGGTTTGCACCACTGCGCACCCGGCTGGAGCACCCAGTGAGGCTACCGTCGCCCCAAAGAAGGATATTCGCATTTACAG
TGATGCGGGCATGACGGGGTTCCTGGAACAGTGGGAGAACGATGATCACATGAAAGGAGACCTTCCAAATCACAAAAGAC
CTTCAGCACCTATCGACTTCTCACAAATCAATCTGGGCAAGCCTGAAAGCACACTGAAAATTATTAAAATAGGCAAGACT
GATGATGTTTGTTACCGTCTCAGGAAGCCCCACTGAGAAGGAGATGAAGGAAATCACCAGCCTGTGACAAGGCAGTTTTT
CAGGGCCAACTACAAAGTCCAGAGTTTATTGTGGGATTTGACTGTGCCATTTTCATGGTG

Alignment

ORF - retro_lafr_505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.2 %
• Parental protein coverage: 75.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAACSWARAVVVLLC-ASDLLLLLLLPPGACAAGDPPGAPGEATPPPRKKKDIRDYNDADMARLLEQWEK
          MA..SWA...V.LL...SDLLLL.LLPP..C....P.GAP.EAT..P..KKDIR.Y.DA.M...LEQWE.
Retrocopy MAVSSWAGVAVLLLS<SSDLLLLRLLPPWVCTTAHPAGAPSEATVAP--KKDIRIYSDAGMTGFLEQWEN

Parental  DDDIEEGDLPEHKRPSAPVDFSQIDPSKPESIL-KMTKKGKTLMMFVTVSGSPTEKEMEEITGLWQGS-L
          DD....GDLP.HKRPSAP.DFSQI...KPES.L.K..K....LMMFVTVSGSPTEKEM.EIT.L.QGS..
Retrocopy DDHMK-GDLPNHKRPSAPIDFSQINLGKPESTL>KLLK*AR-LMMFVTVSGSPTEKEMKEITSL*QGS<F

Parental  FNANYDVQ-RFIVGSDRAIFML
          F.ANY.VQ..FIVG.D.AIFM.
Retrocopy FRANYKVQ<EFIVGFDCAIFMV

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_505 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
Callithrix jacchus	ENSCJAG00000007811	1 retrocopy	retro_cjac_3285,
Homo sapiens	ENSG00000117899	1 retrocopy	retro_hsap_990,
Gorilla gorilla	ENSGGOG00000027583	1 retrocopy	retro_ggor_793,
Loxodonta africana	ENSLAFG00000014513	1 retrocopy	retro_lafr_505 ,
Monodelphis domestica	ENSMODG00000019402	2 retrocopies	retro_mdom_30, retro_mdom_344,
Oryctolagus cuniculus	ENSOCUG00000016290	1 retrocopy	retro_ocun_1947,
Pan troglodytes	ENSPTRG00000007366	1 retrocopy	retro_ptro_759,