RetrogeneDB ID: retro_lafr_895

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_45:7310960..7312928(-)
• Located in intron of: ENSLAFG00000006627

Retrocopy information

• Ensembl ID: ENSLAFG00000013633
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAPOLA
• Ensembl ID: ENSLAFG00000000946
• Aliases: None
• Description: None

Sequence

>retro_lafr_895
GTCAGCACTCAGGGCCCACCACAGACATCGTCGCCCCAGAAGCACTATGGCCTCTCTTCCCCGATCAGTTTAGCAGCCCC
CAAGGAGACTGACTGCATACTTACCCAGAAATTAATTGAAACCCTGAAGCCCTTCGGGGTTTTTGAAGAGGAAGAGGAAC
TGCAGCGCAGGATTTTAATTTTGGAAAAATTAAATAACCTGGTAAAGGAGTGGATACGGGAAATCAGCGAGAGCAAGAAC
CTTCCACAGCCTGTTATTGAAAGTGTTGGAGGAAAGATTTTCACATTTGGATCATACAGATTAGGAGTCCATACAAAAGG
GGCCGATATTGATGCGTTGTGTGTTGCACCAAGACATGTTGACCGAAGTGACTTTTTCACCTCATTCTATGATAAATTGA
AACTACATGAAGAAGTAAAAGATTTAAGGGCTGTTGAAGAGGCATTTGTACCAGTTATCAAACTATGTTTTGATGGGATA
GAGATTGATATTTTGTTCGCAAGATTAGCACTGCAGACTATTCCAGAAGATTTGGACCTGAGAGATGACAGTCTGCTTAA
AAATTTAGATATTAGATGCATAAGAAGTCTTAACGGTTGCCGGGTAACCGATGAAATTTTACACTTAGTACCAAACATTG
ACAACTTCAGGTTAACTCTGAGAGCTATCAAATTGTGGGCCAAATGCCACAATATCTATTCCAATATATTAGGTTTCCTT
GGAGGTGTTTCTTGGGCTATGTTAGTTGCAAGAACTTGCCAGCTTTATCCAAATGCAGTAGCATCAACTCTTGTCCGTAA
ATTTTTCTTGGTATTTTCTGAATGGGAATGGCCAAATCCAGTGCTATTGAAAGAGCCTGAAGAACGGAATCTTAATTTGC
CTGTATGGGACCCAAGGGTCAACCCCAGTGATAGGTACCATCTTATGCCTATAATTACACCAGCATATCCACAGCAGAAC
TCCACTTACAACGTGTCTGTTTCAACACGGATGGTCATGATTGAGGAGTTTAAACAAGGGCTTGCTATCACACATGAAAT
TTTGCTGAGTAAGGCAGAGTGGTCCAAGCTTTTTGAAGCTCCGAACTTCTTTCAAAAGTACAAGCATTACATTGTACTTC
TAGCAAGTGCGCCAACAGAAAAACAACATCTAGAATGGGTGGGCTTGGTGGAATCAAAAATCCGAATTCTGGTTGGAAGC
TTGGAGAAGAATGAATTCATTACCCTGGCACATGTGAACCCCCAGTCATTTCCATCACCCAAGGAAAATCCTGACAAGGA
TGAATTTCGTACAATGTGGGTGATCGGGTTAGTGTTGAAAAAACCAGAAAATTCTGAAACTCTCAGTATTGATCTCACCT
ATGATATTCAGTCTTTCACTGATACAGTTTATAGGCAAGCGATAAACAGCAAGATGTTTGAGATGGATATGAAAATTGAT
GCAGTGCACTTAAGGAGAAGGGAACTTTATCAGCTCCTACCTAATCATGTGCTTCAGAAAAAGAAAACACGTTCAGCAGA
AGGCATCAAATTGACAGCCCTGAATGACAGCAGCCTTGAATTGTCTGTGGACAGTGATGACAGCTTGTCTGTGTCTTCAT
CTACCAGCAGTGTGAAGACCAGTCCATTGACAGGCAGCTCTCAGGGCAGGGGCAGTCCTGGCCCAGTTGTAATGGCAGCA
TCTGTGACCAACATTCAGGCTACTGAGGTTTCCATGCCACAAGGCAATTCCAGTGAAAGCTCGGGGAGTTTTTTAAGTGA
AAGCATTCTTCAAAATACTGCACAACCAGCCATCTCTCCGCCACCAAGGGCCACAGTTGCCAGAGTTGTTTCTTCAACAC
GTCTGATAACCCATCCCCCGAGACCTTCAGGAAACGCAGCAACAAAAATACCTAATCCTATCATAGGAGTCTAGAGAACC
TTCTCCCCTCGAAAAGAAGAAAAGACCAAGAAAACCAAAACAGAAGAA

Alignment

ORF - retro_lafr_895 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.69 %
• Parental protein coverage: 89.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTTQGSQQTRPPQKHYGITSPISLATPKETDCVLTQRLIETLKPFGVFEEEEELQRRILILGKLNNLVKE
          V.TQG..QT..PQKHYG..SPISLA.PKETDC.LTQ.LIETLKPFGVFEEEEELQRRILIL.KLNNLVKE
Retrocopy VSTQGPPQTSSPQKHYGLSSPISLAAPKETDCILTQKLIETLKPFGVFEEEEELQRRILILEKLNNLVKE

Parental  WIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVK
          WIREISESKNLPQ.VIE.VGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKL.EEVK
Retrocopy WIREISESKNLPQPVIESVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLHEEVK

Parental  DLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLV
          DLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLV
Retrocopy DLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLV

Parental  PNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNP
          PNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WEWPNP
Retrocopy PNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWEWPNP

Parental  VLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLS
          VLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.EILLS
Retrocopy VLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHEILLS

Parental  KAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAP
          KAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFP.P
Retrocopy KAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPSP

Parental  KDNPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRRQLH
          K.NPDK.EFRTMWVIGLV.KK.ENSE.LS.DLTYDIQSFTDTVYRQAINSKMFE.DMKI.A.H..RR.L.
Retrocopy KENPDKDEFRTMWVIGLVLKKPENSETLSIDLTYDIQSFTDTVYRQAINSKMFEMDMKIDAVHLRRRELY

Parental  QLLPNHVLQKKKKHSAEGVRLTALNDSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGRNSPAPAVT
          QLLPNHVLQKKK..SAEG..LTALNDSSL.LS.DSD.S.SV.S.TS..KTSPL...GSSQGR.SP.P.V.
Retrocopy QLLPNHVLQKKKTRSAEGIKLTALNDSSLELSVDSDDSLSVSSSTSSVKTSPL--TGSSQGRGSPGPVVM

Parental  AASVTNTQAPEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNQPPRPSGNAAT
          AASVTN.QA.EVS.PQ.NSSESSG...SESI.Q...QPAISPPP..TV.RVVSSTRL...PPRPSGNAAT
Retrocopy AASVTNIQATEVSMPQGNSSESSGSFLSESILQNTAQPAISPPPRATVARVVSSTRLITHPPRPSGNAAT

Parental  KIPNPIAGMKRTSSPHKEESPKKTRTEE
          KIPNPI.G..RT.SP.KEE..KKT.TEE
Retrocopy KIPNPIIGV*RTFSPRKEEKTKKTKTEE

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_895 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000090060	1 retrocopy	retro_hsap_30,
Gorilla gorilla	ENSGGOG00000006287	1 retrocopy	retro_ggor_202,
Loxodonta africana	ENSLAFG00000000946	1 retrocopy	retro_lafr_895 ,
Myotis lucifugus	ENSMLUG00000010922	1 retrocopy	retro_mluc_1396,
Monodelphis domestica	ENSMODG00000012887	2 retrocopies	retro_mdom_1714, retro_mdom_1916,
Mus musculus	ENSMUSG00000021111	1 retrocopy	retro_mmus_37,
Otolemur garnettii	ENSOGAG00000004611	1 retrocopy	retro_ogar_987,
Procavia capensis	ENSPCAG00000004199	1 retrocopy	retro_pcap_91,
Rattus norvegicus	ENSRNOG00000004827	1 retrocopy	retro_rnor_863,