RetrogeneDB ID: retro_lafr_601

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:17922392..17923908(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARS
• Ensembl ID: ENSLAFG00000009855
• Aliases: None
• Description: None

Sequence

>retro_lafr_601
ATACACCTTGAAAAAGGAGGTGTGTCCAGCAATGATTTTTCTTCTTTGGAAGCTTTATGTAAGAAAATCATTAAAGAAAA
ACAAACTTTTGAAAGATTGGAAGTTAAGAAAGAAACTTCACTGGAAATGTTTAAGTATAACAAATTCAAATGCTGGACGC
TGAATGAAAAAGTGAATACTCTAATTACCACAGTCTATAGGTGTGGCCTTTTGATAGATCCCTGCCGGGTCTTCATGTCA
GACGCACTGGTAAAATTAAAACTTTAAAAATGCACAAAATTCCTCCACATATTGGGAAACAAAGCAGATATGGAAACGTT
CCAGAGAATTTATGGCACTTCATTCCCAGATCCTAAAATGTTGAAAGAGTGGGAGAAGTTCTAAAGGGAAGCTAAAAACC
GAGATCATAGGAAAATTGGGAGGGACCAAGAGCTATATTTCTTCCATGAACTCAGCCCTGGAAGTTGCTTTTTCCTGCCA
AAGGGAGCCTACATTTATAATATACTTACCGAGTTTATGAGGAGTGAATATAGGAAATGAGGATTAAAGGAGGTGGTCAC
CCCAAACATCTACAACAGCCAACTCAGGATGACCTCGGAAACTGGCAGCACTACAGTGAGAAAATGTTTTCCTTTGAGGT
GGAGAAGAAGCTATATGCTCTGAAACCCATGAACTGTCCAGAACACTGCATTATGTTTGATCATCAGCCAAGATGCTGGA
GAGAGTTGCCTCTGTGAGTAGCTGATTTGGGGGTACATCATAGGAATGAGATTTCAGGAGCACTCACAGCACTCATCCCT
GTGCAAAGATTTCAGCAGGGTGATGCTCACATATTCTGTGCCATGGAGCAGACTGAGGATGAAATAAAAGGTTGTATGGA
TTTTCTATGTACAGTGTGTAGTGTATTTGGATTTTCTTTTAAACTGAACCTTTCTACTTGCCCAGAAAAATTCCTTGGAG
ATATCGAAGTACAGAATTAAGCTGAGAAACAACTGCGAAATAACCTGAATTAATTTGGTGAAAAGTGGACGTTAAACCCT
GGAGATGGAGCTTTCTATGGTTCAAAGATCGACATACAAATTAAAGGTGCAATTGGTCTATACCACCAGTGTGCAACAAT
CCAGCTGGATTTTCAGATGCCCATCAGATTTAACCTGACTTTTGTAAGCCATGATGGTGGTGATAAGAAAAGACCACTGA
TTGTTCATGGAGCCATCTTGGAATCAGTGGAAAGAATGATTGCTATTCTCACTGAAAACGATGGAGGCAAACGGCCCTTC
TGGCTGTCTCCTCACCATGCAATAGTAGTTCCTGTGGGACCTACGTGTGATGGCTAGGTCCAAAAGATACGGCAAAAACT
CCATCATACTAAATTCACTGTGGATGTTGATCTGGATCCAGGCTGTACCTTGACTAAGATCAGAAATGCCCAGTTGGCAC
AATATAACTTCATTCTAGTTGTTGGTGAGAAAACAGAAAGCAGTGGCATTGTGACATCCGCACAAGAGATAATAAG

Alignment

ORF - retro_lafr_601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.29 %
• Parental protein coverage: 70.36 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MYLEEGGVSSNDFSSLESLCKKIIKEKQAFERLEVKKETLLEMFKYNKFKCRILNEKVNTPTTTVYRCGP
          ..LE.GGVSSNDFSSLE.LCKKIIKEKQ.FERLEVKKET.LEMFKYNKFKC..LNEKVNT..TTVYRCG.
Retrocopy IHLEKGGVSSNDFSSLEALCKKIIKEKQTFERLEVKKETSLEMFKYNKFKCWTLNEKVNTLITTVYRCGL

Parental  LIDLCR-GPHVRHTGKIKTLKIHK-NSSTYWE-GKADMETLQRIYGISFPDPKMLKEWEKFQEEAKNRDH
          LID.CR.G.HVR.TGKIKTLK.HK.NSSTYWE..KADMET.QRIYG.SFPDPKMLKEWEKF..EAKNRDH
Retrocopy LIDPCR<GLHVRRTGKIKTLKMHK<NSSTYWE<NKADMETFQRIYGTSFPDPKMLKEWEKF*REAKNRDH

Parental  RKIGKDQELYFFHELSPGSCFFLPKGAYIYNTLIEFIRSEYRKRGFQEVVTPNIYNSRLWMTS-GHWQHY
          RKIG.DQELYFFHELSPGSCFFLPKGAYIYN.L.EF.RSEYRK.G..EVVTPNIYNS.L.MTS.G.WQHY
Retrocopy RKIGRDQELYFFHELSPGSCFFLPKGAYIYNILTEFMRSEYRK*GLKEVVTPNIYNSQLRMTS<GNWQHY

Parental  SENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDD
          SE.MFSFEVEK.L.ALKPMNCP.HC.MFDH.PR.WRELPL..AD.GV.HRNE.SGALT.L..V.RFQQ.D
Retrocopy SEKMFSFEVEKKLYALKPMNCPEHCIMFDHQPRCWRELPL*VADLGVHHRNEISGALTALIPVQRFQQGD

Parental  AHIFCAMEQIEDEIKGCLDFLRTVYDVFGFSFKLNLSTRPEKFLGDIEVWNQAEKQLENSLNEFGEKWQL
          AHIFCAMEQ.EDEIKGC.DFL.TV..VFGFSFKLNLST.PEKFLGDIEV.N.AEKQL.N.LN.FGEKW.L
Retrocopy AHIFCAMEQTEDEIKGCMDFLCTVCSVFGFSFKLNLSTCPEKFLGDIEVQN*AEKQLRNNLN*FGEKWTL

Parental  NPGDGAFYGPKIDIEIKDAIGRYHQCATIQLDFQLPIRFNLTFVSHDGDDKKRPVIVHRAILGSVERMIA
          NPGDGAFYG.KIDI.IK.AIG.YHQCATIQLDFQ.PIRFNLTFVSHDG.DKKRP.IVH.AIL.SVERMIA
Retrocopy NPGDGAFYGSKIDIQIKGAIGLYHQCATIQLDFQMPIRFNLTFVSHDGGDKKRPLIVHGAILESVERMIA

Parental  ILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQEFHDAKFMADVDLDPGCTLNKKIRNAQLAQYNF
          ILTEN.GGK.PFWLSP....VVPVGPTCD...QK.RQ..H..KF..DVDLDPGCTL..KIRNAQLAQYNF
Retrocopy ILTENDGGKRPFWLSPHHAIVVPVGPTCDG*VQKIRQKLHHTKFTVDVDLDPGCTLT-KIRNAQLAQYNF

Parental  ILVVGEKEKTSGTV-NIRTRDNK
          ILVVGEK...SG.V..IRTRDNK
Retrocopy ILVVGEKTESSGIV<DIRTRDNK

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_601 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000009855	1 retrocopy	retro_lafr_601 ,