RetrogeneDB ID: retro_lafr_604

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_247:204541..205618(+)
• 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_604
CCCTTTATTACCAGTTTCAAGCACCTGTTCAACCCTGTGAAGCCGGCGCGTGGCACCCAGGAGCCAGACTGGCCACGACT
CTCAGGGTTTTTACCTCCTATAACTCCAAGAGAAAAGTTTTTTCTTTCCCAGCTGATGCTGGAACCACCAAGGGAACTCT
TCTAAAAGCACCTTGCCAGATTGCGTTCATGGGTGTTGGAAACAGGGGCCAGTGTGTGGACATAAGTGGGCTTTAAGCAG
CCTTAGCTGAGTGCCAGTCAGAATTGCCAACACAGAGTAAAGCTAGCTTCCCTAGCATTCTCAGTGACCCAGACCTCAAT
TCTTCCAGTTTTGGATTTGACAGCTTGGTTGCCTCTCAAAACACAGAAGCTTTAGTCAGTGGACCAAAACCACCTATTGA
AAGCCATTTTCGACCAGCGTTTTTCTAACACCTCCACTCCATGTGAGGATGAGTTGGCATGGCTAAATCTGACGGAGACT
GACCATGCAATTCAGTGGGATAAGTCAATGTCTGTTAAGAGTAGCACTGGTATAGAGATGAAGCAAACAATGGCCAAAGC
CTTCAAATACCCCTTATCTTCTCCTCAACAAACACGTTCCTTGGTGAGTTGGAAAAAAAATGCAAAACTTGTCTATCATA
TTGGCCTGACTCCAGCCGATCTTCCTGATCTCGTGGAAAACAAGTCTTTAGTTGCTATAGAAATGTTGCTGAAATTAATG
CAGTTGAGCCAGATAACCAAGTATTTTTAAGTGCTGGTCAATATGGACATGTCCTTACATTCAGTGAAAGTTCTAAATCA
GCTAACTACAGCTGTTGATCTACCTCTTGAATTTATCCACCTTTATATATCCAATTACATCTCTACTTGTGAACAATTTA
AGTATCATTTGGTGCACTTTGTCTGTGTCTTCCTCCGATCCTTGATCCGTAACAAAATTATTAATGTGCAGGACTTGTTT
ATAGAAGTGCAGGCATTCTGTATTGAATCCTGTAGGATACGAGAAGCTGCTGGCCTTTTCTGGTTGTTGAAGACATTGGA
TACTGGGGAAACCCCTTCTGAGACTAAAATGTCAAAG

Alignment

ORF - retro_lafr_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.04 %
• Parental protein coverage: 73.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKTVSFIHIATKMPGVTQGVRPPDNLLAQGFLPPITPPEKFFLSQLMLAPPRELF-KKTPRQIALMDVGN
          P...SF.H..........G...PD.....GFLPPITP.EKFFLSQLML.PPRELF..K.P.QIA.M.VGN
Retrocopy PFITSFKHLFNPVKPA-RGTQEPDWPRLSGFLPPITPREKFFLSQLMLEPPRELF<LKAPCQIAFMGVGN

Parental  MGQSVDISGLQLALAERQSELPTQSKASFPSILSDPDPDSSNSGFDSSVASQITEALVSGPKPP-IESHF
          .GQ.VDISGL..ALAE.QSELPTQSKASFPSILSDPD..SS..GFDS.VASQ.TEALVSGPKPP.....F
Retrocopy RGQCVDISGL*AALAECQSELPTQSKASFPSILSDPDLNSSSFGFDSLVASQNTEALVSGPKPP>LKAIF

Parental  RPEFIRPPPPLHVCEDELAWLNPTEPEHTIQWDKSMCVKNSTGVEIKRIMAKAFRSPLSSPQQTQLLGEL
          ...F.....P...CEDELAWLN.TE..H.IQWDKSM.VK.STG.E.K..MAKAF..PLSSPQQT..L...
Retrocopy DQRFSNTSTP---CEDELAWLNLTETDHAIQWDKSMSVKSSTGIEMKQTMAKAFKYPLSSPQQTRSLVSW

Parental  EKDPKLVYHIGLTPAKLPDLVENNPLVAIEMLLKLMQSSQITEYFSVLVNMDMSLHSMEVVNRNRLTTAV
          .K..KLVYHIGLTPA.LPDLVEN..LVAIEMLLKLMQ.SQIT.YF.VLVNMDMSLHS..V.N...LTTAV
Retrocopy KKNAKLVYHIGLTPADLPDLVENKSLVAIEMLLKLMQLSQITKYF*VLVNMDMSLHSVKVLNQ--LTTAV

Parental  DLPPEFIHLYISNCISTCEQIKDKYMQNRLVRLVCVFLQSLIRNKIINVQDLFIEVQAFCIEFSRIREAA
          DLP.EFIHLYISN.ISTCEQ...KY....LV..VCVFL.SLIRNKIINVQDLFIEVQAFCIE..RIREAA
Retrocopy DLPLEFIHLYISNYISTCEQF--KY---HLVHFVCVFLRSLIRNKIINVQDLFIEVQAFCIESCRIREAA

Parental  GLFRLLKTLDTGETPSETKMSK
          GLF.LLKTLDTGETPSETKMSK
Retrocopy GLFWLLKTLDTGETPSETKMSK

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_604 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 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,