RetrogeneDB ID: retro_lafr_518

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:103361872..103362517(+)
• Located in intron of: ENSLAFG00000014082

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM57A
• Ensembl ID: ENSLAFG00000017562
• Aliases: None
• Description: None

Sequence

>retro_lafr_518
ACAACACTGGTTTCTTCAGCGCAAGCTGTGCTGGCCACCGGGTCAGGGATCATCATTATCCGCTCCTGCAAAGATGTGAT
CACTGACAGGCACTGGCTTGCTTGAGAATATGTCTGGTTTTTGAATCCATACATGATCTATGACTACTACGCCATGGACC
TCTGTGAATGGTACAAAACCAAGGATGAGAACCACAGATACTCCCTTACCACTTTTCAAAACTTCGTAAGTCAAAACCAC
CTCATGATCACACACCATGCAGTCATTCTGTTTGCCCTTGTACCTGTTGTGCAGAGGCTTAGGAGAGACCTGGGGGACTT
CTTTGTTGGCTCAATCTTCACGGCAGAACTGAGTACTCATTTTGTGTCACTGGGCAGAGTTCTGATTCAGCTAAAGTAGC
AGCACACCCTCTGTCCAAGCTGGACATAGTCCTCACCCTGGCCACCTTCCTTTCCTGTCAGATCCTTCTTTCCCTTTCAT
GTATTGGTCCTACGGCCGAAAGCAGGGACTAAGCCTGTTCCAAGTGTCATTCCATATCCCTTCCCGCTGCAATGTGGCCA
ATGCCTTCCTCATTACTCCCCAGATCTACTGTTCTCACTGCTGTGCAGGAACGCAGCCTGGCTCTTTGATGCTCCCCAAG
CCAAA

Alignment

ORF - retro_lafr_518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 82.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TRLVSSVQAVLATGSGIIIIRSCKDVVTDRHWLAREYVWFLIPYMIYDYYAMYLCEWYKTKDKSHRHSLT
          T.LVSS.QAVLATGSGIIIIRSCKDV.TDRHWLA.EYVWFL.PYMIYDYYAM.LCEWYKTKD..HR.SLT
Retrocopy TTLVSSAQAVLATGSGIIIIRSCKDVITDRHWLA*EYVWFLNPYMIYDYYAMDLCEWYKTKDENHRYSLT

Parental  VFQNFLSQNRLMITHHAVILFALVPVAQRLRGDLGDFFVGCIFTAELSTPFVSLGRVLIQLKQQHTL-LY
          .FQNF.SQN.LMITHHAVILFALVPV.QRLR.DLGDFFVG.IFTAELST.FVSLGRVLIQLK.QHTL.L.
Retrocopy TFQNFVSQNHLMITHHAVILFALVPVVQRLRRDLGDFFVGSIFTAELSTHFVSLGRVLIQLK*QHTL<LS

Parental  KVNGVLTLATFLSCRILL-FPFMYWSYGQQRGLSLFQVPFHIPFHCNVANAFLIAPQIY-WFSLLCRKAA
          K...VLTLATFLSC.ILL.FPFMYWSYG...GLSLFQV.FHIP..CNVANAFLI.PQIY..FSLLCR.AA
Retrocopy KLDIVLTLATFLSCQILL<FPFMYWSYGRKQGLSLFQVSFHIPSRCNVANAFLITPQIY<LFSLLCRNAA

Parental  RLFGAPQAK
          .LF.APQAK
Retrocopy WLFDAPQAK

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_518 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
Canis familiaris	ENSCAFG00000019129	1 retrocopy	retro_cfam_1644,
Echinops telfairi	ENSETEG00000019235	1 retrocopy	retro_etel_7,
Loxodonta africana	ENSLAFG00000017562	1 retrocopy	retro_lafr_518 ,
Microcebus murinus	ENSMICG00000009347	1 retrocopy	retro_mmur_111,