RetrogeneDB ID: retro_lafr_628

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_265:29636..30462(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF130
• Ensembl ID: ENSLAFG00000008735
• Aliases: None
• Description: None

Sequence

>retro_lafr_628
CAGTGTATCACCTTGCTGCAGAGGGGAAATTGTACATTTAAAGAGAAAATACCATGGACTGCTTTCCACGATGCAGTTGC
TGTAGTCATCTATAATAATAAAGCCAAAGAGGAGCCAGTCACCATGATTCATCCAGGCACTGGAGATATTATTGCTGTCG
TGATTACAGAATTGAGGGGTATGGATACTTTGAGTTATCTGGGAAAAAAATCTCTGTACAAATGACAACAGCTGTTGGAG
CTCGTATGCCAACAAAGAACTTCAGCTGTAGCTCTCTAGTCTTCATGTCAATATCCTTTACTGTTTTGGTGATTATCTCT
TCAGCATGGCTCACATTCTACTTCATTCAGAAGATCAGGTACACAAATGCAAGTGACAGGAACCAGCGTCGTCTAGGAAA
TGCAGCCCAGAAGGCCATCAGCAAATTGACAACCAGGACAGTAAAAAAGGTAATAAGGAAACATACCCTGACTTTGATCA
CTGTGCAATCTGCATAGAGAGCTATAAGCAGAATGATATTGTCCTAATTCTCCCCTGCAAGCATGTTTTCCACAAATCCT
GCATAGATCCCTGGTTTAGTGAAAACTGTACCTGTCCTGTGTGCAAACTTAATATTTTGAAGGCTCTGGGAATTGTGCCA
AATTTGCCATGTATTGATAATAGAACATTTGATATGGAAAGGCTCACCAGAACCCAAGCAGTTAACCAAAAATCAGCCCT
TGGTGACGTTGCCAGCAACTGCTCCCTTGGCCTCAAGCCACTTTGAAGTTTGGGGATATCGCCTCTTCCTCAGGATGGGG
AACGTACTCCTAGAACAGGCGAAATC

Alignment

ORF - retro_lafr_628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.37 %
• Parental protein coverage: 66.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QWIALLQRGNCTFKEKISRAAFHNAVAVVIYNNKSKEEPVTMTHPGTGDIIAVMITELRGKDILSYLEKN
          Q.I.LLQRGNCTFKEKI...AFH.AVAVVIYNNK.KEEPVTM.HPGTGDIIAV.ITELRG.D.LSYL.K.
Retrocopy QCITLLQRGNCTFKEKIPWTAFHDAVAVVIYNNKAKEEPVTMIHPGTGDIIAVVITELRGMDTLSYLGKK

Parental  -ISVQMTIAVGARMPPKNFSRGSLVFVSISFIVLMIISSAWLIFYFIQKIRYTNARDRNQRRLGDAAKKA
          .ISVQMT.AVGARMP.KNFS..SLVF.SISF.VL.IISSAWL.FYFIQKIRYTNA.DRNQRRLG.AA.KA
Retrocopy <ISVQMTTAVGARMPTKNFSCSSLVFMSISFTVLVIISSAWLTFYFIQKIRYTNASDRNQRRLGNAAQKA

Parental  ISKLTTRTVKK-GDKETDPDFDHCAVCIESYKQNDVVRILPCKHVFHKSCVDPWLSEHCTCPMCKLNILK
          ISKLTTRTVKK.G.KET.PDFDHCA.CIESYKQND.V.ILPCKHVFHKSC.DPW.SE.CTCP.CKLNILK
Retrocopy ISKLTTRTVKK<GNKETYPDFDHCAICIESYKQNDIVLILPCKHVFHKSCIDPWFSENCTCPVCKLNILK

Parental  ALGIVPNLPCTDNVAFDMERLTRTQAVNRRSALSDLASDSSLGLEPLRTSGISPLPQDGELTPRTGEI
          ALGIVPNLPC.DN..FDMERLTRTQAVN..SAL.D.AS..SLGL.PL...GISPLPQDGE.TPRTGEI
Retrocopy ALGIVPNLPCIDNRTFDMERLTRTQAVNQKSALGDVASNCSLGLKPL*SLGISPLPQDGERTPRTGEI

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_628 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002816	1 retrocopy	retro_lafr_946,
Loxodonta africana	ENSLAFG00000008735	3 retrocopies	retro_lafr_628 , retro_lafr_876, retro_lafr_969,
Nomascus leucogenys	ENSNLEG00000001941	1 retrocopy	retro_nleu_100,
Sus scrofa	ENSSSCG00000014013	3 retrocopies	retro_sscr_150, retro_sscr_253, retro_sscr_254,