RetrogeneDB ID: retro_lafr_975

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_55:2018918..2019548(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPRE1
• Ensembl ID: ENSLAFG00000015453
• Aliases: None
• Description: None

Sequence

>retro_lafr_975
ATGGCAGTGAACATACAGGTGACATCAGTCACCGGTGATAACCTAAATTGACATGACATGCTGGCTTGGATCAATGAGTC
TCTGCAGTTGAATCTGACAAAGATGGAATGGTTGTACTCACGGGCTGCCTATTGTCAGTTTATGGACATCTGGTCCTTGG
CCTCCATTGTCTTCAAGAAAGTGAAATTCCAAGCTAAGTTAGAACATGAATACACCCGGAACTTTAAAATACTACAAGCA
AGTTTTAAGAGAAGAGTGTTGACAAAATAATTCCAGTGGACAAATTAGCAAAAGGAAAGTTTTGGGGCAATTTTGAATTT
GTCCGTGGTTCAAGAAATTTTTTGATGTAAACCAGGATGGAAAAGACTATGACCCTGTAGCTGCCAGACAAGGTCAGGAA
ACTGCAGTGGCTCTTGCCCTTGTTGCTCCAGCTCTGAGGAAACCAAAGAAACCCTCAGCCCGAGCAGTGCAGCTCCACAG
AGGCTCATTTCAACAGAGAAGTACTGCACCTTCTAAGGCTGGCCCGGGCGTGGGGAGAAAGAGTCCTGGTGTGGAGAGGA
CGAAGCAGCTGACTTGATGCAGCAGGGCAACGTGTTAAAGTTTACCGTCGAAGATTTGGAGAAGGAGAAA

Alignment

ORF - retro_lafr_975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 79.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAVNVYSTSVTSDNLSRHDMLAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQAKLEHE
          MAVN...TSVT.DNL..HDMLAWINESLQLNLTK.E.L.S.AAYCQFMD.....SI..KKVKFQAKLEHE
Retrocopy MAVNIQVTSVTGDNLN*HDMLAWINESLQLNLTKMEWLYSRAAYCQFMDIWSLASIVFKKVKFQAKLEHE

Parental  YIQNFKILQAGFKRM-GVDKIIPVDKLVKGKFQDNFEFVQ-WFKKFFDANYDGKDYDPVAARQGQETAVA
          Y..NFKILQA.FKR...VDKIIPVDKL.KGKF..NFEFV..WFKKFFD.N.DGKDYDPVAARQGQETAVA
Retrocopy YTRNFKILQASFKRR<SVDKIIPVDKLAKGKFWGNFEFVR<WFKKFFDVNQDGKDYDPVAARQGQETAVA

Parental  PSLVAPALSKPKKPLSTSSAAPQRPISTQRTTAASKAG-PGMVRKNPGVGNGDDEAAELMQQVNVLKLTV
          ..LVAPAL.KPKKP.S.......R....QR.TA.SKAG.PG...K....G...DEAA.LMQQ.NVLK.TV
Retrocopy LALVAPALRKPKKP-SARAVQLHRGSFQQRSTAPSKAG<PGRGEKESWCG--EDEAADLMQQGNVLKFTV

Parental  EDLEKER
          EDLEKE.
Retrocopy EDLEKEK

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_975 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 21 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013238	3 retrocopies	retro_amel_1187, retro_amel_1436, retro_amel_848,
Canis familiaris	ENSCAFG00000007306	13 retrocopies	retro_cfam_1338, retro_cfam_1554, retro_cfam_1665, retro_cfam_1804, retro_cfam_1808, retro_cfam_2084, retro_cfam_2163, retro_cfam_241, retro_cfam_547, retro_cfam_762, retro_cfam_774, retro_cfam_806, retro_cfam_913,
Choloepus hoffmanni	ENSCHOG00000006737	10 retrocopies	retro_chof_1064, retro_chof_1075, retro_chof_1113, retro_chof_1138, retro_chof_1514, retro_chof_2248, retro_chof_2557, retro_chof_2591, retro_chof_643, retro_chof_704,
Callithrix jacchus	ENSCJAG00000015601	10 retrocopies	retro_cjac_1424, retro_cjac_1647, retro_cjac_1946, retro_cjac_2077, retro_cjac_2084, retro_cjac_2366, retro_cjac_2861, retro_cjac_3259, retro_cjac_3271, retro_cjac_3308,
Cavia porcellus	ENSCPOG00000023542	1 retrocopy	retro_cpor_194,
Dasypus novemcinctus	ENSDNOG00000007431	2 retrocopies	retro_dnov_730, retro_dnov_822,
Felis catus	ENSFCAG00000007783	2 retrocopies	retro_fcat_1335, retro_fcat_970,
Gorilla gorilla	ENSGGOG00000022496	1 retrocopy	retro_ggor_2765,
Loxodonta africana	ENSLAFG00000015453	1 retrocopy	retro_lafr_975 ,
Microcebus murinus	ENSMICG00000001965	3 retrocopies	retro_mmur_1125, retro_mmur_1179, retro_mmur_129,
Myotis lucifugus	ENSMLUG00000016403	6 retrocopies	retro_mluc_1212, retro_mluc_1811, retro_mluc_1812, retro_mluc_1883, retro_mluc_635, retro_mluc_931,
Macaca mulatta	ENSMMUG00000001816	2 retrocopies	retro_mmul_1938, retro_mmul_2374,
Monodelphis domestica	ENSMODG00000019445	3 retrocopies	retro_mdom_1213, retro_mdom_1946, retro_mdom_431,
Mustela putorius furo	ENSMPUG00000017867	3 retrocopies	retro_mputfur_1240, retro_mputfur_1304, retro_mputfur_341,
Oryctolagus cuniculus	ENSOCUG00000024265	1 retrocopy	retro_ocun_582,
Otolemur garnettii	ENSOGAG00000026557	2 retrocopies	retro_ogar_226, retro_ogar_2290,
Ochotona princeps	ENSOPRG00000006707	4 retrocopies	retro_opri_1161, retro_opri_1162, retro_opri_1212, retro_opri_807,
Pteropus vampyrus	ENSPVAG00000015887	1 retrocopy	retro_pvam_1035,
Tarsius syrichta	ENSTSYG00000000833	1 retrocopy	retro_tsyr_2018,
Tursiops truncatus	ENSTTRG00000014809	2 retrocopies	retro_ttru_1683, retro_ttru_1917,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,