RetrogeneDB ID: retro_lafr_524

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:17158137..17158892(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000017110
• Aliases: None
• Description: None

Sequence

>retro_lafr_524
GTGGGAACCATGGAGGGTGTCAAAGAGAAGAAAAAGAAGTTTCCTGCTGTGCCAGAAACCCTTAAGAAAAACGAAGGAAT
TTTGCAGAACTAAAGATCAAGCACCTAAGAAAGAAGTTTGCCCAAAGGATGCTTCAAAAGGCAAGGAGGAAGCTTATCTA
TGAGAAAGTTAAGCACTATCACAAGGAATACAGGCAAATGTACAGTAGGACTGAGATTTGAATGGCTAGGATGGCAAGAA
AAGCTGGCAACTTCTACGTACCTGCAGAACCCAGATTGGCATTTGTTATCAGGATCAGAGGTATCAATGGTGTGAGCCCA
AAGGTTCAAAAGGTGTTTCAGCTTCTTCGCCTTTGCCAGATCTTCAACGGCACCTTTGTTAAGCTCAATAAGGCTTCGAT
TAACATGCTAAGAATCTGTGGAACCATATGTTGCATGGGGGTACCCAAACCTGAAATCAGTGAATGAACTGATCTGTAAG
TGTGGTTATGGCAAAATCAATAAGAAGCAAATTGCCCTGACAGGTAACACTTTGATTGCACCATCTCTTGGTAAATATGG
CATCATCTGCATGGAGGATCTGATTCATGAGATCTATACTGTTGGGAAACACTTCAAAGAAGCAAACAACTTCCTGTAGC
CCTTCAAATTAGCTTCTCCGCAAGGTGGAATGAAGAAAGAGGCCCCCCGTTTTGTAGAAGGTGGAGATGCTGGCAACGGG
GAAGACCAGATCAACAGCTTATTAGAAGGATGAAC

Alignment

ORF - retro_lafr_524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.49 %
• Parental protein coverage: 96.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IGRKPGRREKKKKVPDVPETLKK-KRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMY-
          .G...G..EKKKK.P.VPETLKK.KRRNFAELKIK.LRKKFAQ.ML.KARRKLIYEK.KHYHKEYRQMY.
Retrocopy VGTMEGVKEKKKKFPAVPETLKK<KRRNFAELKIKHLRKKFAQRMLQKARRKLIYEKVKHYHKEYRQMYS

Parental  RTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRI
          RTEI.MARMARKAGNFYVPAEP.LAFVIRIRGINGVSPKV.KV.QLLRL.QIFNGTFVKLNKASINMLRI
Retrocopy RTEI*MARMARKAGNFYVPAEPRLAFVIRIRGINGVSPKVQKVFQLLRLCQIFNGTFVKLNKASINMLRI

Parental  -VEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGKYGIICMEDLIHEIYTVGKRFKEA
          .VEPY.AWGYPNLKSVNELI.K.GYGKINKK.IALT.NTLIA.SLGKYGIICMEDLIHEIYTVGK.FKEA
Retrocopy >VEPYVAWGYPNLKSVNELICKCGYGKINKKQIALTGNTLIAPSLGKYGIICMEDLIHEIYTVGKHFKEA

Parental  NNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQIN-RLIRRMN
          NNFL.PFKL.SP.GGMKK....FVEGGDAGN.EDQIN..LIRRMN
Retrocopy NNFL*PFKLASPQGGMKKEAPRFVEGGDAGNGEDQIN<QLIRRMN

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_524 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 8 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017654	15 retrocopies	retro_dnov_1561, retro_dnov_1692, retro_dnov_182, retro_dnov_1893, retro_dnov_209, retro_dnov_2158, retro_dnov_2568, retro_dnov_264, retro_dnov_2657, retro_dnov_279, retro_dnov_287, retro_dnov_365, retro_dnov_655, retro_dnov_77, retro_dnov_971,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Loxodonta africana	ENSLAFG00000017110	10 retrocopies	retro_lafr_140, retro_lafr_169, retro_lafr_334, retro_lafr_462, retro_lafr_47, retro_lafr_524 , retro_lafr_694, retro_lafr_707, retro_lafr_816, retro_lafr_909,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Oryctolagus cuniculus	ENSOCUG00000008407	12 retrocopies	retro_ocun_109, retro_ocun_1164, retro_ocun_1282, retro_ocun_1342, retro_ocun_1494, retro_ocun_1646, retro_ocun_1879, retro_ocun_456, retro_ocun_501, retro_ocun_718, retro_ocun_727, retro_ocun_785,
Pteropus vampyrus	ENSPVAG00000009292	10 retrocopies	retro_pvam_105, retro_pvam_109, retro_pvam_1192, retro_pvam_1221, retro_pvam_151, retro_pvam_287, retro_pvam_308, retro_pvam_68, retro_pvam_69, retro_pvam_995,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209, retro_sscr_796,