RetrogeneDB ID: retro_lafr_291

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_11:43459304..43460118(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASP6
• Ensembl ID: ENSLAFG00000002727
• Aliases: None
• Description: None

Sequence

>retro_lafr_291
ATGACAGAAACACACGCCTTTTACAGAAGTGAAACATTTGATTTAGCAGAAAAGTGTAAATGGACCACTGGAAAAGAGGA
ATTGCTTTAATTTTCCATCATGAGAGGTTCTTCTGGAGCTTAACACTACCAGAAGGGTGTTGCACCAGTGCAGACAATCT
TAAACAAAGGCTTTGAGATCTAGAGTTTGAAGTGAAACGCTTTAAGGACCTTAAAGTGGAAGGACTACCGCTCCAAATTC
AAGAGGTATTGACCTCTGACCTTATAGAAACTGATTGCTTGTTATCTGTATTCCTGAGTCATGGTGAAGGCAGGCACATT
TATGCATACGATACAAAAATGGAAATTCAGACATTGACTGGTTTGTTCAAAAGGGACAAACGTTAGAGCCTGGTTGGAAA
ACCCAAGATACTCATTATCCAGGCGGGTCAAGGAGACCAGCACAATGTGCCAGTCATTGCTTTGGATGTTGTGAATCCAC
AGACAAACAAGCTGGACACGAACGTAACTGAGGTGGATGCGGCCTCTGTTTACAGGCTACCTGCTGGAGCAAACTTCTTC
ATGTGTTCCTGTGTTGCAGAAGGTTATTATTCTCACCCAGAAACTGTGACCAGGTCACAGCACGTTCAAGATTTGCCTGA
CGTGTTGGGAAAATAGTTTCCTCCTTAGAGTTCACAGAACTCACGCTGGTGAACAGATAAGTTCCTCGGCACTGGGTGGA
CTTTTGCAAAGACCCAAGTGCAATTGGAAAGAAACAGGTTCCCTGCTTTGCCCCAATGCTTACTAAAAAGCTACATTTCT
TTCCAAAATCTAAA

Alignment

ORF - retro_lafr_291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTETDAFYRSETFDPAEKYK-MDHGKRGVALIFNHERFFWHLTLPERRGTCADRDNLKRRLLDLGFEVKC
          .TET.AFYRSETFD.AEK.K.MDH.KRG.ALIF.HERFFW.LTLPE..G.C...DNLK.RL.DL.FEVK.
Retrocopy MTETHAFYRSETFDLAEKCK<MDHWKRGIALIFHHERFFWSLTLPE--GCCTSADNLKQRL*DLEFEVKR

Parental  FNDLKAEELLLQIHEVSTSSHTDADCFLCVFLSHGEGNHIYAYDAKIKIQTLTGLFKGDKCQSLVGKPKI
          F.DLK.E.L.LQI.EV.TS.....DC.L.VFLSHGEG.HIYAYD.K..IQTLTGLFK.DK..SLVGKPKI
Retrocopy FKDLKVEGLPLQIQEVLTSDLIETDCLLSVFLSHGEGRHIYAYDTKMEIQTLTGLFKRDKR*SLVGKPKI

Parental  FIIQACRGNQHDVPVLPLDAVDHPTDKPDGNVTEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSW
          .IIQA..G.QH.VPV..LD.V...T.K.D.NVTEVDAASVY.LPAGA.F.MC..VAEGYYSH.ETV..S.
Retrocopy LIIQAGQGDQHNVPVIALDVVNPQTNKLDTNVTEVDAASVYRLPAGANFFMCSCVAEGYYSHPETVTRSQ

Parental  YIQDLCEML-EKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPKSK
          ..QDL...L..K..SSLEFTE.LTLVNR.V....VDFCKDPSAIGKKQVPCFA.MLTKKLHFFPKSK
Retrocopy HVQDLPDVL<GKIVSSLEFTE-LTLVNR*VPRHWVDFCKDPSAIGKKQVPCFAPMLTKKLHFFPKSK

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_291 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002727	1 retrocopy	retro_lafr_291 ,
Microcebus murinus	ENSMICG00000010297	2 retrocopies	retro_mmur_709, retro_mmur_844,
Monodelphis domestica	ENSMODG00000005948	1 retrocopy	retro_mdom_1854,
Vicugna pacos	ENSVPAG00000009840	1 retrocopy	retro_vpac_431,