RetrogeneDB ID: retro_lafr_192

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:84184938..84185628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1L2
• Ensembl ID: ENSLAFG00000029587
• Aliases: None
• Description: None

Sequence

>retro_lafr_192
ATGCCTAAGTTAGAATCTCCTAAAGATCCTGAACAGCTGTGGAAACTCTTCATCGGAGGGTTGAGCTTTGAAACAGCAGA
TGAGAGTCTGAGGAGCCGTTTTGAACAATGGGGGAAGCTCACAAACTGTGTGATACCAAGAGATCCAAAGGCCAAGTGCT
CCAAAGCTTTTGGTTTGTCACTTTAATTCTACTGTGGAGGTAGTAGGCGCAGCCATGATCAGGCCACACAAGGTGGATGG
AAGAGTTGTAGAAACAAAGAGGGCTGTCTCACGAGAAGAATCTCAAAGACTAGGCACCCCCTTAACTGTGAAAAAAATCT
TTGTTGGTAGTATTTAAGAAGAAACTGAATAACATCACCTAAGAGATTATTTTGAGCAGTATGGGGAAATTGATGTGATT
GAAATCATGACTAACCAAGGCAGTGGCAAGAAGAGGGGTTTTGCTTTGTAACTTTTGATGACCATGACTCTGTAGATAAG
ATCGTCATTCAGAAATACCCTACGATGAATGGTCACAACTGAGAAGTAAGGGAAGCCCTACCAAAGCAAGAGATGACCAG
TGCCTCATCCAGTGAAAGAGGTAGAAGCAGTTTTGGAAATTTTGGTGGTGGCCCTGGAGGTAGTTTTGGTGGGAATGACA
ACTTTGGTCATGGAGGAAACTACAGTGGGAGAGATGGCTTTGGTGGCAAC

Alignment

ORF - retro_lafr_192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.25 %
• Parental protein coverage: 71.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT-YSTVEEVD
          M.K.ESPK.PEQL.KLFIGGLSFET.DESLRS.FEQWG.LT.CV..RDP..K.S..FG.....STVE.V.
Retrocopy MPKLESPKDPEQLWKLFIGGLSFETADESLRSRFEQWGKLTNCVIPRDPKAKCSKAFGLSL>NSTVEVVG

Parental  AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD
          AAM..RPHKVDGRVVE.KRAVSRE.SQR.G..LTVKKIFVG.I.E.TE.HHLRDYFEQYG.I.VIEIMT.
Retrocopy AAM-IRPHKVDGRVVETKRAVSREESQRLGTPLTVKKIFVGSI*EETE*HHLRDYFEQYGEIDVIEIMTN

Parental  RGSGKKRGFA-FVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGG
          .GSGKKRGFA.FVTFDDHDSVDKIVIQKY.T.NGHN.EVR.AL.KQEM.SASSS.RGRS..GNFGGG.GG
Retrocopy QGSGKKRGFA<FVTFDDHDSVDKIVIQKYPTMNGHN*EVREALPKQEMTSASSSERGRSSFGNFGGGPGG

Parental  GFGGNDNFGRGGNFSGRGGFGGS
          .FGGNDNFG.GGN.SGR.GFGG.
Retrocopy SFGGNDNFGHGGNYSGRDGFGGN

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_192 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 13 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Loxodonta africana	ENSLAFG00000001189	1 retrocopy	retro_lafr_405,
Loxodonta africana	ENSLAFG00000008612	1 retrocopy	retro_lafr_650,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Loxodonta africana	ENSLAFG00000029587	5 retrocopies	retro_lafr_1202, retro_lafr_1208, retro_lafr_192 , retro_lafr_747, retro_lafr_961,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,
Procavia capensis	ENSPCAG00000001867	5 retrocopies	retro_pcap_111, retro_pcap_162, retro_pcap_377, retro_pcap_424, retro_pcap_435,
Pongo abelii	ENSPPYG00000025850	4 retrocopies	retro_pabe_1765, retro_pabe_2285, retro_pabe_3492, retro_pabe_3835,
Ictidomys tridecemlineatus	ENSSTOG00000006551	8 retrocopies	retro_itri_1291, retro_itri_1567, retro_itri_190, retro_itri_354, retro_itri_439, retro_itri_446, retro_itri_456, retro_itri_515,
Tursiops truncatus	ENSTTRG00000004505	27 retrocopies	retro_ttru_1202, retro_ttru_1223, retro_ttru_1251, retro_ttru_1331, retro_ttru_1362, retro_ttru_156, retro_ttru_157, retro_ttru_1678, retro_ttru_1732, retro_ttru_1806, retro_ttru_1813, retro_ttru_1874, retro_ttru_221, retro_ttru_311, retro_ttru_479, retro_ttru_599, retro_ttru_605, retro_ttru_607, retro_ttru_620, retro_ttru_63, retro_ttru_678, retro_ttru_708, retro_ttru_812, retro_ttru_882, retro_ttru_902, retro_ttru_926, retro_ttru_981,