RetrogeneDB ID: retro_lafr_646

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_28:3543783..3544226(-)
• Located in intron of: ENSLAFG00000017072

Retrocopy information

• Ensembl ID: ENSLAFG00000030038
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CALM3
• Ensembl ID: ENSLAFG00000001155
• Aliases: None
• Description: calmodulin 3 (phosphorylase kinase, delta) [Source:HGNC Symbol;Acc:1449]

Sequence

>retro_lafr_646
GCTGACCAACTGACTGAAGAGCAGATTGCAGAATTCAAAGAAGCCTTTTCACTATTTGACAAGGATGGTGATGGAACTAT
AACAACAAAGGAATTGGGAACTGTAATGAGGTCTCTTGGGCAGAATCCCACAGAAGCAGAATTACAGGACATGATTAATG
AAGTAGACACTGATGGTAATGGCACGATTGACTTCCTGGAATTTCTGACAATGATGGCAAGAAAAATGAAAGACACAGAC
AGTGAAGAAGAAATTAGAGAAGCATTCCGTGTGTTCGATAAGGATGGCAATGGCTATATCAGTGCAGCGGAGCTTCGCCA
TTGATGACAAACCTTGGCGAGAAGTTAACAGATGAAGAGGTTGATGAAATGATCAGGGAAGCAGACATTGACGGTGATGG
TCAAGTAAACTATGAAGAGTTTGTACAAATGATGACAGCAAAG

Alignment

ORF - retro_lafr_646 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.32 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLT
          ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVD.DGNGTIDF.EFLT
Retrocopy ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDTDGNGTIDFLEFLT

Parental  MMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRH-VMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
          MMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRH..MTNLGEKLTDEEVDEMIREADIDGDGQVNYE
Retrocopy MMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRH<LMTNLGEKLTDEEVDEMIREADIDGDGQVNYE

Parental  EFVQMMTAK
          EFVQMMTAK
Retrocopy EFVQMMTAK

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_646 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 25 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015712	1 retrocopy	retro_acar_45,
Ailuropoda melanoleuca	ENSAMEG00000008565	3 retrocopies	retro_amel_1209, retro_amel_1562, retro_amel_421,
Bos taurus	ENSBTAG00000014583	2 retrocopies	retro_btau_113, retro_btau_135,
Canis familiaris	ENSCAFG00000029151	4 retrocopies	retro_cfam_121, retro_cfam_164, retro_cfam_225, retro_cfam_68,
Cavia porcellus	ENSCPOG00000001612	1 retrocopy	retro_cpor_1316,
Erinaceus europaeus	ENSEEUG00000000140	1 retrocopy	retro_eeur_468,
Echinops telfairi	ENSETEG00000009377	5 retrocopies	retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Felis catus	ENSFCAG00000004995	1 retrocopy	retro_fcat_1726,
Homo sapiens	ENSG00000160014	3 retrocopies	retro_hsap_1255, retro_hsap_1785, retro_hsap_59,
Gorilla gorilla	ENSGGOG00000000212	4 retrocopies	retro_ggor_187, retro_ggor_2234, retro_ggor_522, retro_ggor_988,
Loxodonta africana	ENSLAFG00000001155	5 retrocopies	retro_lafr_100, retro_lafr_156, retro_lafr_631, retro_lafr_646 , retro_lafr_86,
Loxodonta africana	ENSLAFG00000002905	1 retrocopy	retro_lafr_1165,
Loxodonta africana	ENSLAFG00000009865	1 retrocopy	retro_lafr_655,
Microcebus murinus	ENSMICG00000013180	3 retrocopies	retro_mmur_1032, retro_mmur_1447, retro_mmur_501,
Myotis lucifugus	ENSMLUG00000010528	1 retrocopy	retro_mluc_2477,
Monodelphis domestica	ENSMODG00000009222	1 retrocopy	retro_mdom_1126,
Mustela putorius furo	ENSMPUG00000005261	1 retrocopy	retro_mputfur_404,
Mus musculus	ENSMUSG00000019370	3 retrocopies	retro_mmus_2879, retro_mmus_3448, retro_mmus_454,
Nomascus leucogenys	ENSNLEG00000002752	2 retrocopies	retro_nleu_1407, retro_nleu_3097,
Otolemur garnettii	ENSOGAG00000014764	2 retrocopies	retro_ogar_2085, retro_ogar_3311,
Procavia capensis	ENSPCAG00000005751	1 retrocopy	retro_pcap_7,
Petromyzon marinus	ENSPMAG00000003323	1 retrocopy	retro_pmar_12,
Pongo abelii	ENSPPYG00000010154	4 retrocopies	retro_pabe_1106, retro_pabe_1466, retro_pabe_3238, retro_pabe_3676,
Pelodiscus sinensis	ENSPSIG00000013173	1 retrocopy	retro_psin_9,
Ictidomys tridecemlineatus	ENSSTOG00000014352	1 retrocopy	retro_itri_1018,