RetrogeneDB ID: retro_lafr_530

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:49870108..49870791(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMAP1
• Ensembl ID: ENSLAFG00000007948
• Aliases: None
• Description: None

Sequence

>retro_lafr_530
TTGAGTGATGATTTGGGAATCACTGAGATAATGACTTATAATTCCTTACAGGAACTGTTATGCCCCAGGTCAAGGGATGC
CCCCTGTACCAGAAGCTCCCAACTGTCTGCACTAGTGTCTGGGGATCTGTATCTATTCACTGACTAAACTACAACACCAG
AAGAATAAGCAAAGAAGCAACTTTCCAAAGACTCTGTCTTATTTCTGTATGGTACAGGAACTATTCAGCAGCAGGATATT
CCTGATGAGTTTATGAGACTCCCAAAATACAGCATTTACCTTACAAGCACCAACTAATTTCAAGGTTTTCCATCAGTGGG
TGTGCCTGTGCCTGCAGCTTCTAGATTAAAGAAAACGGGATGGGACAGAGTGCAACCACAATGGTGGACATACTCTTGCC
CAGCAAGTTTATGGAAAACGTACAAACTGGTGTGATGCCATACCCTCAAAATGCTGTTGGGCCCCAAGCACAAATGGTGT
GACAGATGGGTGCACCCTAGAGTATGTTTGGCCTGCGGCAAGTTCAGCAGTCTCAGTGGAGCTTCTCACAGAAGAATTGG
TAGATATCTGACATGGGTATCAAACATTCAAACTCTGCAGTGGGTTTTGGCCAGCCCTCAAGCACAACAGCAGGATGGTC
AGGAAGCTCATGGGATTAGACTCTTAGCACACAACTGCGGAAA

Alignment

ORF - retro_lafr_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.28 %
• Parental protein coverage: 53.15 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LNDDLDIFGPMISNPLPTTVMPPAQGTLTVPAAAPLSIAPGDLDLFTEQTTKAEESTKKQLSKDSILSLY
          L.DDL.I...M..N.L.....P..................GDL.LFT..TT..EE..KKQLSKDS.L.LY
Retrocopy LSDDLGITEIMTYNSLQELLCPRSRDAPCTRSSQLSALVSGDLYLFTD*TTTPEE*AKKQLSKDSVLFLY

Parental  GTGTIQQQNTPGMFM-GPANIPFTSQAPPAF-QGFPSMGVPVPAAPGLMG-NVMGQSASMMVGMPMPNGF
          GTGTIQQQ..P..FM....N..FT.QAP..F.QGFPS.GVPVPAA..L...N.MGQSA..MV....P..F
Retrocopy GTGTIQQQDIPDEFM>DSQNTAFTLQAPTNF<QGFPSVGVPVPAASRLKK<NGMGQSATTMVDILLPSKF

Parental  MGSAQTGVMPLPQNVAGPQGGMVGQMGASQSKFGLPQTQQPQWSLSQMNQQMAGMSINSANPAVGFGQPP
          M...QTGVMP.PQN..GPQ..MV.QMGA..S.FGL.Q.QQ.QWS.SQ.N.....M.I...N.AVGFGQP.
Retrocopy MENVQTGVMPYPQNAVGPQAQMV*QMGAP*SMFGLRQVQQSQWSFSQKNW*ISDMGIKHSNSAVGFGQPS

Parental  STTAGWSGSSSGQTLSTQLWK
          STTAGWSGSS...TLSTQL.K
Retrocopy STTAGWSGSSWD*TLSTQLRK

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_530 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000001865	1 retrocopy	retro_etel_1525,
Felis catus	ENSFCAG00000007247	1 retrocopy	retro_fcat_1157,
Loxodonta africana	ENSLAFG00000007948	1 retrocopy	retro_lafr_530 ,
Mus musculus	ENSMUSG00000026155	1 retrocopy	retro_mmus_3253,