RetrogeneDB ID: retro_lafr_654

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_29:32334823..32335158(+)
• Located in intron of: ENSLAFG00000017665

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM32A
• Ensembl ID: ENSLAFG00000009394
• Aliases: None
• Description: None

Sequence

>retro_lafr_654
ATGGTGGCCTATGAGCAGGTCCAGAAGGGGACCTAAAACTGAAAGGCATCACAGGGCTTGGTGTGACCAAGCGGAAGAAG
AAAAAGAAGGACAATGACAGTACGAAACTTCTGGAAGCGATGGGAATGAGCAAAACGAACTAGGAGGAGAGGCAGTACAG
CCTGGACAAGAGGACGCTGGCCCAAGTGGCCTTCGAGAAGCTGCAGATAAAGCAGCAAACAGAAAGGATCCTGAAGAAGA
CACCCAAAACCCACAAGCAGAGAGTGGAGAACATCAACAGATACCTGGACACCCTCACAGAACATCACATCATCTTCAAA
GTCAGCTGGACCAAG

Alignment

ORF - retro_lafr_654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAYEQVQKGP-LKLKGVAELGVTKRKKKK-DKDKAKLLEAMGTSKKNEEEKRRGLDKRTPAQAAFEKMQ
          M.AYEQVQKG..LKLKG...LGVTKRKKKK.D.D..KLLEAMG.SK.N.EE....LDKRT.AQ.AFEK.Q
Retrocopy MVAYEQVQKGT<LKLKGITGLGVTKRKKKKKDNDSTKLLEAMGMSKTN*EERQYSLDKRTLAQVAFEKLQ

Parental  EKRQMERILKKASKTHKQRVEDFNRHLDTLTEHYDIPKVSWTK
          .K.Q.ERILKK..KTHKQRVE..NR.LDTLTEH..I.KVSWTK
Retrocopy IKQQTERILKKTPKTHKQRVENINRYLDTLTEHHIIFKVSWTK

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_654 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 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046846	1 retrocopy	retro_btau_312,
Callithrix jacchus	ENSCJAG00000014097	4 retrocopies	retro_cjac_15, retro_cjac_2459, retro_cjac_288, retro_cjac_979,
Homo sapiens	ENSG00000105058	4 retrocopies	retro_hsap_1116, retro_hsap_1950, retro_hsap_2541, retro_hsap_693,
Gorilla gorilla	ENSGGOG00000022418	4 retrocopies	retro_ggor_1420, retro_ggor_1587, retro_ggor_592, retro_ggor_872,
Loxodonta africana	ENSLAFG00000009394	1 retrocopy	retro_lafr_654 ,
Microcebus murinus	ENSMICG00000013721	3 retrocopies	retro_mmur_1449, retro_mmur_252, retro_mmur_500,
Myotis lucifugus	ENSMLUG00000000585	2 retrocopies	retro_mluc_2147, retro_mluc_59,
Monodelphis domestica	ENSMODG00000014904	1 retrocopy	retro_mdom_1401,
Mustela putorius furo	ENSMPUG00000016048	1 retrocopy	retro_mputfur_1493,
Mus musculus	ENSMUSG00000003039	2 retrocopies	retro_mmus_1612, retro_mmus_3017,
Nomascus leucogenys	ENSNLEG00000005441	3 retrocopies	retro_nleu_192, retro_nleu_2227, retro_nleu_2790,
Oryctolagus cuniculus	ENSOCUG00000002238	1 retrocopy	retro_ocun_1275,
Otolemur garnettii	ENSOGAG00000027763	2 retrocopies	retro_ogar_3348, retro_ogar_949,
Pan troglodytes	ENSPTRG00000010641	4 retrocopies	retro_ptro_1304, retro_ptro_1480, retro_ptro_497, retro_ptro_684,
Rattus norvegicus	ENSRNOG00000039528	1 retrocopy	retro_rnor_105,
Sus scrofa	ENSSSCG00000013855	2 retrocopies	retro_sscr_292, retro_sscr_870,
Tarsius syrichta	ENSTSYG00000009106	1 retrocopy	retro_tsyr_418,