RetrogeneDB ID: retro_lafr_1041

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:80759608..80760084(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL2
• Ensembl ID: ENSLAFG00000010579
• Aliases: None
• Description: None

Sequence

>retro_lafr_1041
TCTGGAGTTACAGTGAATGATGAAGTCATCAAAGTTTTTAATGATGTGAAAGTAAGGAAATCTTCTACACAAGAGATCTA
AAAAAGAAAGAAGGCAGTCCTCTTCTGTTTAAGTGATGACAAAAGGCAAATAATTGTAGAGGAAGCAAACCAGATCTTGG
TGGTGATACCATAGAGGACCCCTACACATCTTTTGTGAAGTTGCTACCTCAGAATGATTGCTGGTAGGCTTTGCACGACA
CCACAGATGAAACAAAAGAGCCTAAGAAAGAAGACCTAGTATTTATATTCTGGGCTTCTGAAAGTGTACCTTTAAAAAGC
AAGATGATTTATGCAAGCTCTAAAGATGCCATTAAAAAGAAATTTACAGATATTAAATATGAGTGGCAAGTAAATGGCTT
GGATGATATTAAAGACCGCTTGACACTCAGAGAGAGATTAGAAGGCAATGTGGTAGTTTCACTTGAAGGGAAACCC

Alignment

ORF - retro_lafr_1041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.37 %
• Parental protein coverage: 98.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGVTVNDEVIKVFNDMKVRKSSTQEEIKKRKKAVLFCLSDDKRQIIVEEAKQILV-GDIGDTVEDPYTSF
          SGVTVNDEVIKVFND.KVRKSSTQE.I.KRKKAVLFCLSDDKRQIIVEEA.QILV.GD...T.EDPYTSF
Retrocopy SGVTVNDEVIKVFNDVKVRKSSTQE-I*KRKKAVLFCLSDDKRQIIVEEANQILV<GD---TIEDPYTSF

Parental  VKLLPLNDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKFTGIKHEWQVNGLD
          VKLLP.NDC..AL.D.T.ETKE.KKEDLVFIFWA.ES.PLKSKMIYASSKDAIKKKFT.IK.EWQVNGLD
Retrocopy VKLLPQNDCW*ALHDTTDETKEPKKEDLVFIFWASESVPLKSKMIYASSKDAIKKKFTDIKYEWQVNGLD

Parental  DIKDRSTLGEKLGGNVVVSLEGKP
          DIKDR.TL.E.L.GNVVVSLEGKP
Retrocopy DIKDRLTLRERLEGNVVVSLEGKP

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_1041 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 19 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015508	1 retrocopy	retro_amel_1347,
Canis familiaris	ENSCAFG00000032562	1 retrocopy	retro_cfam_1006,
Cavia porcellus	ENSCPOG00000008996	1 retrocopy	retro_cpor_1003,
Echinops telfairi	ENSETEG00000006010	3 retrocopies	retro_etel_1579, retro_etel_1622, retro_etel_684,
Felis catus	ENSFCAG00000008480	2 retrocopies	retro_fcat_1223, retro_fcat_1395,
Latimeria chalumnae	ENSLACG00000018011	1 retrocopy	retro_lcha_23,
Loxodonta africana	ENSLAFG00000010579	1 retrocopy	retro_lafr_1041 ,
Macropus eugenii	ENSMEUG00000000739	11 retrocopies	retro_meug_1026, retro_meug_1138, retro_meug_125, retro_meug_1266, retro_meug_1666, retro_meug_1791, retro_meug_2025, retro_meug_2062, retro_meug_210, retro_meug_321, retro_meug_668,
Microcebus murinus	ENSMICG00000009237	1 retrocopy	retro_mmur_493,
Monodelphis domestica	ENSMODG00000012949	1 retrocopy	retro_mdom_171,
Mus musculus	ENSMUSG00000062929	1 retrocopy	retro_mmus_660,
Otolemur garnettii	ENSOGAG00000032321	1 retrocopy	retro_ogar_2346,
Pteropus vampyrus	ENSPVAG00000002798	1 retrocopy	retro_pvam_398,
Rattus norvegicus	ENSRNOG00000045892	1 retrocopy	retro_rnor_684,
Sarcophilus harrisii	ENSSHAG00000004732	1 retrocopy	retro_shar_528,
Sus scrofa	ENSSSCG00000001959	2 retrocopies	retro_sscr_1198, retro_sscr_327,
Ictidomys tridecemlineatus	ENSSTOG00000001675	3 retrocopies	retro_itri_1313, retro_itri_581, retro_itri_632,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,
Vicugna pacos	ENSVPAG00000003273	1 retrocopy	retro_vpac_644,