RetrogeneDB ID: retro_lafr_998

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_586:30057..31058(+)
• 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_998
TTGCAGCCAACACCTTTGTTACCAGTTTCAGGCACCTGTTCAACCCTGTGAAGCCTGCGCGTGGTGGCCAGGAGCCAGAC
TGACCACGACTCTCAGGATTTTTACCTCCTATAACTCCAACAGAACAGTTTTTTCTTTCCCAGCTAATGCTGGAACCATC
AAGGGAACTCTTTTAAAAGCACCTCGCCAGATTGCTTTCATGGGTGTTGGAAACAGGGGTCAGTGTGTGGACTTAAGTGG
GCTTCAAGTAGCCTTAGCTGAGTGCCAGTCAGAATTGCCAACGCAGAGTAAAGCTAGCTTCCCTAGCATTCTCAGTGACC
CAGACCTCAATTCTTCCATTTTTGGATTTGACAGTTTGGTTGCCTCTCAAAACACAGAAGCTTTAGTCAGTGGACCAAAA
CCACCTATTGAAAGCCATTTTCGGCTAGCGTTTTTCTAACACCTCCACTCCATGTTTGTGAGGATGAGTTGGCATGGCTA
AATCCAACGGAGACCGACCATGCAATTCAGTGGGATAAGTCAATGTCTGTTAAGAATAGCACTGGTATAGAGATGAAGCA
GATAATGGCCAAAGCCTTCAAATACCCCTTATCTTCTCCTCAACAAACACATTCCTTGGTGAGTTGAAAAAAAATGCAAA
ACTTGTTTATCATATTGGCCTGACTCCAGCCAATCCTCCTGATCTCCTGGAAAACAAGTCTCTAGTTGCTATAGAAATGT
TGCTGAAATTAATGCAGTTGAACCAGATAACCGAGTATTTTTAAGTGCTGGTCAATATCGACATGTCCTTACATTCAATG
GAAGTTGTAAATCAGTTAACTACAGCTGTTGATCTACCTCTTGAATTTATCCACCTTTATATATCCAATTGCATCTCTAC
TTGTGAACAATTTAAGGGTCATTTGGTGCACCTTGTCTGTGTCTTCCTCCAATCCTTGATCTGTAACGAAATTATTAATG
TGCAGGACTTGTTTATAGAAGTTCAGGCATTCTGTATTGAA

Alignment

ORF - retro_lafr_998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.51 %
• Parental protein coverage: 67. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LKPVPK-TVSFIHIATKMPGVTQGVRPPDNLLAQGFLPPITPPEKFFLSQLMLAPPRELF-KKTPRQIAL
          L.P.P....SF.H..........G...PD.....GFLPPITP.E.FFLSQLML.P.RELF..K.PRQIA.
Retrocopy LQPTPL<VTSFRHLFNPVKPA-RGGQEPD*PRLSGFLPPITPTEQFFLSQLMLEPSRELF<LKAPRQIAF

Parental  MDVGNMGQSVDISGLQLALAERQSELPTQSKASFPSILSDPDPDSSNSGFDSSVASQITEALVSGPKPPI
          M.VGN.GQ.VD.SGLQ.ALAE.QSELPTQSKASFPSILSDPD..SS..GFDS.VASQ.TEALVSGPKPPI
Retrocopy MGVGNRGQCVDLSGLQVALAECQSELPTQSKASFPSILSDPDLNSSIFGFDSLVASQNTEALVSGPKPPI

Parental  ESHFRPEF-IRPPPPLHVCEDELAWLNPTEPEHTIQWDKSMCVKNSTGVEIKRIMAKAFRSPLSSPQQTQ
          ESHFR..F....PP.LHVCEDELAWLNPTE..H.IQWDKSM.VKNSTG.E.K.IMAKAF..PLSSPQQT.
Retrocopy ESHFRLAF<FLTPP-LHVCEDELAWLNPTETDHAIQWDKSMSVKNSTGIEMKQIMAKAFKYPLSSPQQTH

Parental  -LLGELEKDPKLVYHIGLTPAKLPDLVENNPLVAIEMLLKLMQSSQITEYFSVLVNMDMSLHSMEVVNRN
          ..LGEL.K..KLVYHIGLTPA..PDL.EN..LVAIEMLLKLMQ..QITEYF.VLVN.DMSLHSMEVV..N
Retrocopy <FLGELKKNAKLVYHIGLTPANPPDLLENKSLVAIEMLLKLMQLNQITEYF*VLVNIDMSLHSMEVV--N

Parental  RLTTAVDLPPEFIHLYISNCISTCEQIKDKYMQNRLVRLVCVFLQSLI--RNKIINVQDLFIE
          .LTTAVDLP.EFIHLYISNCISTCEQ.K........V.L........I......I.VQ...IE
Retrocopy QLTTAVDLPLEFIHLYISNCISTCEQFKGHLVHLVCVFLQSLICNEIINVQDLFIEVQAFCIE

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_998 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,