RetrogeneDB ID: retro_lafr_371

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_14:9682133..9682667(+)
• Located in intron of: ENSLAFG00000009347

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSLAFG00000030853
• Aliases: None
• Description: None

Sequence

>retro_lafr_371
ATGGCGCAGGATCAAGGTAAAAAACAATACCCCATGCGGGAACTTGGCATCTGTGAGCTCTGCCTCAACATCTTTATGGG
GGAGAGTGGAGACAGACTGTCCTGGGCAGCCAAGGTGTTGGAGCAGCTCATAGGCCAGGCCCCTGTGTTCCGCAAAGCTA
GATACACCGTCAGATTCCTTGGCATTAGGAGAAACGAAAAAATTGCCGTCTACTAGACGGTCCATGGGGCCAAGGTAGTA
AAAATCTTGGAGAAAGGTCTAAAGGTGTGGGAGCATGAATTAAGAAAAAATAATTTCTCAGACACTGGAAATTTTGGTTT
TGGGGTCCAGGAACACATCAATCTGGGGATCAAATATGACCCTACCATTGTTATCTATGGCCTGGCCTTCTATGTGGTGC
TGGGCAGGTCAGATTTCAGCAGGGCAGACAAAAAGTGCAGGACAGGGAGCATTGGGGCCAAACACAGAATCAGCAAAGAG
AAGGCCATGTGCTGATTCCAGCAGAAGTATGATGGGATCATCCTTGCCAGAAAA

Alignment

ORF - retro_lafr_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.69 %
• Parental protein coverage: 98.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKGEIGMSF-GVRERFRSQP
          ..QDQG.K..PMREL.I..LCLNI..GESGDRL..AAKVLEQL.GQ.PVF.K......F.G.R.......
Retrocopy MAQDQGKKQYPMRELGICELCLNIFMGESGDRLSWAAKVLEQLIGQAPVFRKARYTVRFLGIRRNEKIAV

Parental  SFSLMGLMLMNVITAFSSQVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGF
          .....G.............V.E.ELRKNNFSDTGNFGFG.QEHI.LGIKYDP.I.IYGL.FYVVLGR..F
Retrocopy Y*TVHGAKVVKILEK-GLKVWEHELRKNNFSDTGNFGFGVQEHINLGIKYDPTIVIYGLAFYVVLGRSDF

Parental  SIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
          S.ADKK.RTG.IGAKHRISKE.AM..FQQKYDGIIL..K
Retrocopy SRADKKCRTGSIGAKHRISKEKAMC*FQQKYDGIILARK

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_371 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 18 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020905	1 retrocopy	retro_btau_267,
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Callithrix jacchus	ENSCJAG00000020953	1 retrocopy	retro_cjac_790,
Dasypus novemcinctus	ENSDNOG00000011230	2 retrocopies	retro_dnov_1453, retro_dnov_605,
Homo sapiens	ENSG00000142676	6 retrocopies	retro_hsap_1159, retro_hsap_1801, retro_hsap_2272, retro_hsap_3238, retro_hsap_606, retro_hsap_712,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Loxodonta africana	ENSLAFG00000030853	2 retrocopies	retro_lafr_371 , retro_lafr_434,
Macropus eugenii	ENSMEUG00000013738	3 retrocopies	retro_meug_488, retro_meug_517, retro_meug_633,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica	ENSMODG00000012828	1 retrocopy	retro_mdom_641,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus	ENSOANG00000000321	1 retrocopy	retro_oana_49,
Oryctolagus cuniculus	ENSOCUG00000022928	1 retrocopy	retro_ocun_1387,
Pongo abelii	ENSPPYG00000001736	6 retrocopies	retro_pabe_1478, retro_pabe_1946, retro_pabe_2686, retro_pabe_612, retro_pabe_615, retro_pabe_964,
Pteropus vampyrus	ENSPVAG00000004282	1 retrocopy	retro_pvam_1068,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Sus scrofa	ENSSSCG00000024260	4 retrocopies	retro_sscr_1048, retro_sscr_1049, retro_sscr_1074, retro_sscr_819,
Tarsius syrichta	ENSTSYG00000001349	6 retrocopies	retro_tsyr_1138, retro_tsyr_127, retro_tsyr_1583, retro_tsyr_1605, retro_tsyr_516, retro_tsyr_520,