RetrogeneDB ID: retro_lafr_632

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_27:26391520..26392140(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NECAP1
• Ensembl ID: ENSLAFG00000002979
• Aliases: None
• Description: None

Sequence

>retro_lafr_632
CAAGTATCAAAGGAGCTCTTTGCTCAGGCACCAATAGAACAATATTCTGGCACTGCTGAGAAGACAGTGACAGATTCCAA
CTTCTATTTTGTAACCAAATCCAGGATGGCACTAGGTATAGTGCTTTCATTGTCACTAGCCTCATAAATTAGGGTGAAGT
CTTCAACTTTAATATCTTTTTCTAAGATCGCTTCAAGTGGGTAAAGCAGGTATCAAGATGTCCAAAGAATCTCAGGAACC
AGACACTCATCCCACGTAGTACCTGGGCTTCAAGGGAGAACAGACCATCAAGCTGACTAACGGGACCATTATGACCAAGA
AGAGAAGTGACTGCAAGCCCAGGACTGCAGGGACTGGAGACATAGGTGTGCTTACACTCCCACCTGAAGAAGTCACTACT
CCTCCACGGTCCTCTGCTTTTGCCACCAGCAATCACGTCAGCCCACCACCCATGAAAAATCTAACCATGGAGGTGGTGAT
ACAGTTATCTTTTTAAGCAGGGGTTCTCCTGCTCCTGTCACATCGCCAGCACCAGCTCCATGGGCAATGATTTGGGAGAC
TTTAACACTACATCCCGCTCTGTTCCAAACCAGGCACCACAGCCATCCTACAGAGTCCAG

Alignment

ORF - retro_lafr_632 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.63 %
• Parental protein coverage: 77.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KVSGELFAQAPVEQYPGIAVETVADSSRYFVIR-IQDGTGRSAFIGIGFTDRGDAFDFNVSLQDHFKWQR
          .VS.ELFAQAP.EQY.G.A..TV.DS..YFV...IQDGT..SAFI.......G..F.FN....D.FKW..
Retrocopy QVSKELFAQAPIEQYSGTAEKTVTDSNFYFVTK<IQDGTRYSAFIVTSLIN*GEVFNFNIFF*DRFKWVK

Parental  EAC-SNSRLSEAMDTRPKLDLGFKEGQTIKLSIGNITTKKGGASKPRTAGPGGLSLLPPPPGGKVTIPPP
          ......S..S...DT.P...LGFK..QTIKL..G.I.TKK....KPRTAG.G....L..PP...VT.PP.
Retrocopy QVS<KMSKESQEPDTHPT*YLGFKGEQTIKLTNGTIMTKKRSDCKPRTAGTGDIGVLTLPPE-EVTTPPR

Parental  SSSVAISNHVTPPPIP-KSNHGGSDADILLDLDSPAPVVTPAPAPV-SASNDLWGDFSTASSSVSNQAPQ
          SS..A.SNHV.PPP...KSNHGG.D..I.L...SPAPV..P..AP..S..NDL.GDF.T.S.SV.NQAPQ
Retrocopy SSAFATSNHVSPPPMK<KSNHGGGDTVIFLSRGSPAPVTSP--APA<SMGNDL-GDFNTTSRSVPNQAPQ

Parental  PSSWVQ
          PS..VQ
Retrocopy PSYRVQ

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_632 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016989	1 retrocopy	retro_amel_1016,
Canis familiaris	ENSCAFG00000013930	1 retrocopy	retro_cfam_780,
Choloepus hoffmanni	ENSCHOG00000008087	3 retrocopies	retro_chof_1692, retro_chof_1818, retro_chof_1913,
Dasypus novemcinctus	ENSDNOG00000014778	2 retrocopies	retro_dnov_613, retro_dnov_986,
Homo sapiens	ENSG00000089818	1 retrocopy	retro_hsap_3839,
Gorilla gorilla	ENSGGOG00000010233	1 retrocopy	retro_ggor_2585,
Loxodonta africana	ENSLAFG00000002979	1 retrocopy	retro_lafr_632 ,
Mustela putorius furo	ENSMPUG00000016742	1 retrocopy	retro_mputfur_361,
Nomascus leucogenys	ENSNLEG00000001743	1 retrocopy	retro_nleu_1974,
Oryctolagus cuniculus	ENSOCUG00000004309	1 retrocopy	retro_ocun_606,
Otolemur garnettii	ENSOGAG00000006358	1 retrocopy	retro_ogar_3442,
Pongo abelii	ENSPPYG00000004238	1 retrocopy	retro_pabe_3059,
Pan troglodytes	ENSPTRG00000023277	1 retrocopy	retro_ptro_2615,
Rattus norvegicus	ENSRNOG00000009236	1 retrocopy	retro_rnor_1806,
Ictidomys tridecemlineatus	ENSSTOG00000010153	2 retrocopies	retro_itri_1107, retro_itri_740,
Tursiops truncatus	ENSTTRG00000014260	1 retrocopy	retro_ttru_1035,