RetrogeneDB ID: retro_lafr_376

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_14:26535991..26536703(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000004696
• Aliases: None
• Description: None

Sequence

>retro_lafr_376
AAGGCCAAGAATGAGGAGTGGCCCTGCATCACCAAGTTTGGCAGCCTGGTCAAAAACATGAAAACCAAGTCCCTAGAAGA
GATCTGTCTCTTCCCCTGCCCATCAAGGATTCTGAAATCGTTATATTTTCCTGGGGATGCCCCTCCAGGAAACGGTTTTG
AAAATTATGGCCAACTAAAAGCAAACTGGCATTGGCTAGAGGAGCAGGATCAAAGCATTTGTCGCCATTGGGACTACATC
GGCCTCCTCGGTCAGGGCGTGAAGTGCCCCAAGGGCATGGCAGAAACCATCTGTGGGGCCATCATCCTGGCTAAGCTTTC
CATTTCCCTCTTGCCTGGGTGAGGCTACTGGGGGAACAGGATCTGCAAGCACAACACTGTTCCCGGCAAGGTAACTGGCC
TCTGTGGCTTTGTGCTAGTGCACCTCATCCCCATCCCCAAGGACAACGAAAGGGTTTTGCCCCGGTGCCCAAGAAGCTGC
TGCTGATGGTCGATATTGATGACTGCTATGCCTTGGACAGGGGTTGAACTGCCACCTTGAGCAACTTTGCCAGGGCCAAA
TTCTATGCCATCTCCAAACCTACAGCTGTGTTATGCACCATCTCTGGAAGTAGATCTTGTTCACCAAGTGGCTTTACCAG
GAATTCATTGATCATTTTGTAAAGACTCACACCAGAGTCTCTGTGCAGAGGACCAGGCTTCAACTTTTGGCA

Alignment

ORF - retro_lafr_376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.45 %
• Parental protein coverage: 81.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KAEDKEWLPVTKLGRLVKDMKIKSLEEIYLFS-LPIKESEIIDF-FLGMALKDEVLKIMPVQKQTRAGQR
          KA...EW...TK.G.LVK.MK.KSLEEI.LF..LPIK.SEI..F.FLGM.L...VLKIM...KQT..G.R
Retrocopy KAKNEEWPCITKFGSLVKNMKTKSLEEICLFP<LPIKDSEIVIF<FLGMPLQETVLKIMAN*KQTGIG*R

Parental  TRFKAFVAIG-DYNGHVGLGVKCSKEVATAIRGAIILAKL--SIVPVRRGYWGNKIGKPHTVPCKVTGRC
          .R.KAFVAIG.DY.G..G.GVKC.K..A..I.GAIILAKL..S..P...GYWGN.I.K..TVP.KVTG.C
Retrocopy SRIKAFVAIG<DYIGLLGQGVKCPKGMAETICGAIILAKLSISLLP-G*GYWGNRICKHNTVPGKVTGLC

Parental  GSVLVRLIPAPRGTGIVS-APVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISK-TYSYLTPDLW
          G.VLV.LIP.P.....V..APVPKKLL.M..IDDCY...RG.TATL.NFA.A.F.AISK.TYS.....LW
Retrocopy GFVLVHLIPIPKDNERVL<APVPKKLLLMVDIDDCYALDRG*TATLSNFARAKFYAISK<TYSCVMHHLW

Parental  KETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVA
          K...FTK..YQEF.DH.VKTHTRVSVQRT.....A
Retrocopy K*ILFTKWLYQEFIDHFVKTHTRVSVQRTRLQLLA

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_376 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 15 parental genes, and 102 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Bos taurus	ENSBTAG00000009535	7 retrocopies	retro_btau_1236, retro_btau_1420, retro_btau_1656, retro_btau_317, retro_btau_590, retro_btau_661, retro_btau_956,
Canis familiaris	ENSCAFG00000019472	19 retrocopies	retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012, retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Loxodonta africana	ENSLAFG00000004696	11 retrocopies	retro_lafr_1072, retro_lafr_1092, retro_lafr_1103, retro_lafr_174, retro_lafr_284, retro_lafr_327, retro_lafr_376 , retro_lafr_75, retro_lafr_801, retro_lafr_812, retro_lafr_917,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Myotis lucifugus	ENSMLUG00000011660	1 retrocopy	retro_mluc_76,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Mustela putorius furo	ENSMPUG00000015547	11 retrocopies	retro_mputfur_1100, retro_mputfur_1209, retro_mputfur_1212, retro_mputfur_1214, retro_mputfur_1391, retro_mputfur_1497, retro_mputfur_1566, retro_mputfur_369, retro_mputfur_540, retro_mputfur_624, retro_mputfur_931,
Mus musculus	ENSMUSG00000044533	1 retrocopy	retro_mmus_148,
Procavia capensis	ENSPCAG00000002090	2 retrocopies	retro_pcap_251, retro_pcap_433,
Rattus norvegicus	ENSRNOG00000014179	12 retrocopies	retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tursiops truncatus	ENSTTRG00000011393	12 retrocopies	retro_ttru_1341, retro_ttru_1346, retro_ttru_1414, retro_ttru_149, retro_ttru_1762, retro_ttru_1816, retro_ttru_37, retro_ttru_375, retro_ttru_419, retro_ttru_650, retro_ttru_719, retro_ttru_872,
Vicugna pacos	ENSVPAG00000006867	6 retrocopies	retro_vpac_114, retro_vpac_164, retro_vpac_220, retro_vpac_354, retro_vpac_379, retro_vpac_518,