RetrogeneDB ID: retro_lafr_137

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:39016816..39017750(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2ORF29
• Ensembl ID: ENSLAFG00000006411
• Aliases: None
• Description: None

Sequence

>retro_lafr_137
AAAAAAGGTCAAGGCCAGATTGCTTTGATGGACGTTGGAAACATGGGCCAGTCTGTGGACATCAGCGGGCTTCAGCTAGC
CTTAGCAGAGCACCAGTCAGAATTGCCAACCCAGAGTAAAGCTAGCTTCCCTAGTATTCTCAGTGACCCAGACCCAGATT
CTTCCAATTCTGGATTTGACAGCTGGGTCGCCTCTCAGGTCACAGAAGCTTTAGTCAGTGGACCAAAACCTCCTATTGAA
AGCCATTTTCGGCCAGAGTTCATTCATCCTCCGCCTCCACTCCATGTTTGTGAGGACAAGTTGGCATGGCTGAACCCCAC
AGAGGCCGAGCACACCATTCAGTGGGTAAGTCAATGTGTGTTAAGAACAGCACTGGTGTGGAGATCAAGCAAATAATGGC
CAAAGCCTTCAGAAGCCCCTTATCTTCTCCTCAGCAAACACAGCTTCTTGGTGAGTTGGAAAAAGATCCCAAACTTGTTT
ATCATATTGGCCTGACTCCCGCCAAACTTCCTGATCTCTTGGAAAACAACCCTCTAGTTTCCATAGAAATGTTGCTGAAA
TTAATGCAGTCAAGCCAGATAACTGAGTATTTCTCAGTCCTGGTCAATATGGACATGTCCTTACATTCAATGGAAGTTGT
AAATCGACTAACTACAGCTGTTGATCTACCTCCTGAATTTATCCACCTTTATATATAAAATTGCATCTCTACTTGTGAAC
AAATTAAAGATAAATATATGCAGAATCTTTTGGTGCGTCTTGTTTGTGTCTTCCTCCAGTCCTTGATCCATAACAGAATT
ATTAACGTGTAGGACTTGTTTATAGAAGTGCAGGCCTTCTGTATTGAATTCAGTAGGATAGAAGCTGCTGGCCTTTCCCG
GTTGTTAAGACATTGGATACTGGGGAAACCCCTTCTGAGGCTAAAATGTCAAAG

Alignment

ORF - retro_lafr_137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 62.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKTPRQIALMDVGNMGQSVDISGLQLALAERQSELPTQSKASFPSILSDPDPDSSNSGFDSSVASQITEA
          KK...QIALMDVGNMGQSVDISGLQLALAE.QSELPTQSKASFPSILSDPDPDSSNSGFDS.VASQ.TEA
Retrocopy KKGQGQIALMDVGNMGQSVDISGLQLALAEHQSELPTQSKASFPSILSDPDPDSSNSGFDSWVASQVTEA

Parental  LVSGPKPPIESHFRPEFIRPPPPLHVCEDELAWLNPTEPEHTIQW-DKSMCVKNSTGVEIKRIMAKAFRS
          LVSGPKPPIESHFRPEFI.PPPPLHVCED.LAWLNPTE.EHTIQW..KSMCVKNSTGVEIK.IMAKAFRS
Retrocopy LVSGPKPPIESHFRPEFIHPPPPLHVCEDKLAWLNPTEAEHTIQW<GKSMCVKNSTGVEIKQIMAKAFRS

Parental  PLSSPQQTQLLGELEKDPKLVYHIGLTPAKLPDLVENNPLVAIEMLLKLMQSSQITEYFSVLVNMDMSLH
          PLSSPQQTQLLGELEKDPKLVYHIGLTPAKLPDL.ENNPLV.IEMLLKLMQSSQITEYFSVLVNMDMSLH
Retrocopy PLSSPQQTQLLGELEKDPKLVYHIGLTPAKLPDLLENNPLVSIEMLLKLMQSSQITEYFSVLVNMDMSLH

Parental  SMEVVNRNRLTTAVDLPPEFIHLYISNCISTCEQIKDKYMQNRLVRLVCVFLQSLIRNKIINVQDLFIEV
          SMEVV..NRLTTAVDLPPEFIHLYI.NCISTCEQIKDKYMQN.LVRLVCVFLQSLI.N.IINV.DLFIEV
Retrocopy SMEVV--NRLTTAVDLPPEFIHLYI*NCISTCEQIKDKYMQNLLVRLVCVFLQSLIHNRIINV*DLFIEV

Parental  QAFCIEFSRIREAAGLFRLL-KTLDTGETPSETKMSK
          QAFCIEFSRI.EAAGL.RLL.KTLDTGETPSE.KMSK
Retrocopy QAFCIEFSRI-EAAGLSRLL<KTLDTGETPSEAKMSK

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_137 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 2 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000006411	7 retrocopies	retro_lafr_1004, retro_lafr_1005, retro_lafr_137 , retro_lafr_355, retro_lafr_581, retro_lafr_604, retro_lafr_998,
Oryctolagus cuniculus	ENSOCUG00000004448	1 retrocopy	retro_ocun_1950,