RetrogeneDB ID: retro_lafr_1215

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:35390574..35390885(+)
• Located in intron of: ENSLAFG00000021369

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKA2
• Ensembl ID: ENSLAFG00000003405
• Aliases: None
• Description: spindle and kinetochore associated complex subunit 2 [Source:HGNC Symbol;Acc:28006]

Sequence

>retro_lafr_1215
GCTGATTCTGATTTGGATTGTATTCTGTACAAGCTGGAATATGAAACCAGAACAATTATCCTGATGCTGCTGGTGTGAAA
AATCCTGTTACACTCTTAAAGGAATTGTCAGCAGTAAAGTCTCAATATCAGACTTTGCATACATGGTTTAAACCAACTGC
TTTTGAACAGAAAGAGACAAAGGGCTACATTTGTGTTACTTTGAACAAGACTATGACCATGATACAAGAACTACAAAAGC
TAACAGACCTGGAGCTGTCACCACTGACTGAAGAAAACTGCAGAAAAGCAATTAAAGTCTTAATGCCAGAC

Alignment

ORF - retro_lafr_1215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.83 %
• Parental protein coverage: 97.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADSDLDCILYRLEYEIK-NNHPDSAGAKNPVTLLKELSAIKSRYQTLHTRFKPIAVEQKKTKDHICVTLN
          ADSDLDCILY.LEYE...NN.PD.AG.KNPVTLLKELSA.KS.YQTLHT.FKP.A.EQK.TK..ICVTLN
Retrocopy ADSDLDCILYKLEYETR<NNYPDAAGVKNPVTLLKELSAVKSQYQTLHTWFKPTAFEQKETKGYICVTLN

Parental  KTMTMIQELRKLIELELLPLTEEEETAEKQLKAHMPD
          KTMTMIQEL.KL..LEL.PLT..EE...K..K..MPD
Retrocopy KTMTMIQELQKLTDLELSPLT--EENCRKAIKVLMPD

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_1215 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 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021680	2 retrocopies	retro_btau_310, retro_btau_945,
Canis familiaris	ENSCAFG00000029233	1 retrocopy	retro_cfam_766,
Cavia porcellus	ENSCPOG00000006051	1 retrocopy	retro_cpor_542,
Dipodomys ordii	ENSDORG00000010768	2 retrocopies	retro_dord_103, retro_dord_281,
Equus caballus	ENSECAG00000015007	1 retrocopy	retro_ecab_987,
Felis catus	ENSFCAG00000022802	1 retrocopy	retro_fcat_1111,
Homo sapiens	ENSG00000182628	1 retrocopy	retro_hsap_4214,
Loxodonta africana	ENSLAFG00000003405	1 retrocopy	retro_lafr_1215 ,
Myotis lucifugus	ENSMLUG00000010942	1 retrocopy	retro_mluc_83,
Monodelphis domestica	ENSMODG00000014619	1 retrocopy	retro_mdom_347,
Mustela putorius furo	ENSMPUG00000015241	1 retrocopy	retro_mputfur_1435,
Mus musculus	ENSMUSG00000020492	2 retrocopies	retro_mmus_370, retro_mmus_778,
Otolemur garnettii	ENSOGAG00000026072	4 retrocopies	retro_ogar_1882, retro_ogar_2937, retro_ogar_3032, retro_ogar_907,
Rattus norvegicus	ENSRNOG00000025981	3 retrocopies	retro_rnor_1606, retro_rnor_523, retro_rnor_733,
Sorex araneus	ENSSARG00000011128	2 retrocopies	retro_sara_60, retro_sara_662,
Ictidomys tridecemlineatus	ENSSTOG00000024169	4 retrocopies	retro_itri_1115, retro_itri_1275, retro_itri_1434, retro_itri_725,
Tarsius syrichta	ENSTSYG00000006158	3 retrocopies	retro_tsyr_1620, retro_tsyr_2034, retro_tsyr_748,
Tursiops truncatus	ENSTTRG00000017196	1 retrocopy	retro_ttru_143,