RetrogeneDB ID: retro_lafr_1015

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:61324285..61324550(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000006849
• Aliases: None
• Description: None

Sequence

>retro_lafr_1015
GCTAAACACACCAAGAAGGTCAGGATCATCGGTAAACATGGGACCTGTTATGGCACCTCCCTCAGGAAAATGGTGAAGAA
AATTGAAATCAGCCAGCATGCAAGTACACTTGCTCCTTCTGTGGCAAAACCAAGATGAAGTGACGAGCTGTGGGATCTGG
CACTGTGGTTCCTTCATGAGAACAGTAGCCAGTGGGGCCTGGACCTATGCCACTACTTCTGCAGTCACAGTACAATCTGC
CCTCAGAAGACTGAAGGGATTGAAA

Alignment

ORF - retro_lafr_1015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.42 %
• Parental protein coverage: 96.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHA-KYTCSFCGKTKMKRRAV-GIWHCGSCMKTVAGGAW
          AK.TKKV.I.GK.GT.YG.SLRKMVKKIEISQHA.KYTCSFCGKTKMK.RAV.GIWHCGS.M.TVA.GAW
Retrocopy AKHTKKVRIIGKHGTCYGTSLRKMVKKIEISQHA<KYTCSFCGKTKMK*RAV<GIWHCGSFMRTVASGAW

Parental  TYNTTSAVTVKSAIRRLKELK
          TY.TTSAVTV.SA.RRLK.LK
Retrocopy TYATTSAVTVQSALRRLKGLK

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_1015 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 10 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003377	24 retrocopies	retro_amel_109, retro_amel_1170, retro_amel_1197, retro_amel_1204, retro_amel_1248, retro_amel_1310, retro_amel_1349, retro_amel_1534, retro_amel_1597, retro_amel_1724, retro_amel_1815, retro_amel_1910, retro_amel_1929, retro_amel_248, retro_amel_424, retro_amel_428, retro_amel_475, retro_amel_482, retro_amel_606, retro_amel_737, retro_amel_809, retro_amel_83, retro_amel_920, retro_amel_942,
Callithrix jacchus	ENSCJAG00000012417	7 retrocopies	retro_cjac_1060, retro_cjac_1514, retro_cjac_159, retro_cjac_237, retro_cjac_3178, retro_cjac_335, retro_cjac_888,
Equus caballus	ENSECAG00000012046	6 retrocopies	retro_ecab_220, retro_ecab_48, retro_ecab_552, retro_ecab_735, retro_ecab_741, retro_ecab_803,
Latimeria chalumnae	ENSLACG00000011578	1 retrocopy	retro_lcha_71,
Loxodonta africana	ENSLAFG00000006849	5 retrocopies	retro_lafr_1010, retro_lafr_1015 , retro_lafr_109, retro_lafr_987, retro_lafr_991,
Macropus eugenii	ENSMEUG00000004680	23 retrocopies	retro_meug_1094, retro_meug_111, retro_meug_1120, retro_meug_1289, retro_meug_1302, retro_meug_1399, retro_meug_1600, retro_meug_1705, retro_meug_2021, retro_meug_2061, retro_meug_2143, retro_meug_2173, retro_meug_24, retro_meug_290, retro_meug_458, retro_meug_463, retro_meug_496, retro_meug_502, retro_meug_571, retro_meug_691, retro_meug_813, retro_meug_814, retro_meug_83,
Myotis lucifugus	ENSMLUG00000000762	1 retrocopy	retro_mluc_208,
Otolemur garnettii	ENSOGAG00000000817	3 retrocopies	retro_ogar_1317, retro_ogar_3003, retro_ogar_69,
Petromyzon marinus	ENSPMAG00000000001	1 retrocopy	retro_pmar_11,
Pteropus vampyrus	ENSPVAG00000006102	12 retrocopies	retro_pvam_1074, retro_pvam_1346, retro_pvam_169, retro_pvam_204, retro_pvam_343, retro_pvam_48, retro_pvam_652, retro_pvam_658, retro_pvam_669, retro_pvam_761, retro_pvam_765, retro_pvam_90,