RetrogeneDB ID: retro_lafr_527

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:27749799..27750511(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000030676
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CRYZ
• Ensembl ID: ENSLAFG00000011371
• Aliases: None
• Description: None

Sequence

>retro_lafr_527
GTTTTTACTACTAGCACTGTCTCTGGGGACCATGCAGAGTATGTTGTTGCAGCGGATCACATGATTTACTCACTGCCAGA
AAGAATGGACTTTAAACAAGGAGCTGCTATTGGTGTCTCTTACTTTACTGCTTATCTAGTTCTGCTCCGCAGTGCTCCTG
TGAGAGCTGGAGAAATTGTTCTGGTTCCTGGGGCTTGCGGAAGAGTTGGACTAGCAACATGCCAAATTGCTAGAACTTAT
GGCTTAAAGGTTTTGGGTACAGCTGGTACAGAGAAAAGTCAAAACATCATTTTGCAAAATAGAGCCCATGAAGCATTTAA
TTGCAAAGACGTTAGTTATACTGATGAAATTAAGAAGTCTGTTCATGATAAAGGAACTGATATGATTATTGAAATGCTAG
CTAAGGTAAACTTTAGTAATGATTTGAAGCTTTTGTCATGTGGAGGGCGAGTAATAATTGTCGGCAGCAGAGGTTCTATT
GAGATGAACCCGTGGGAAACCATGGCAAAGGAAGCCTAGAATAATTGGAGTTGCTCACTTTTCATCATCCTTGGGGGAAT
TTCAGCAGTTTGCAGCAGCCCTTCAAGCTGGGATGGAAATCGGTTGGTTGAAACCTGTAATATACTCTCAGTATCCATTG
GAGAAAGTAGCACAAGCTCAGGAAAATATCATTTATGGCAGCAGGGCTGCTGGAAAAATTATCTTTCCCTTA

Alignment

ORF - retro_lafr_527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.06 %
• Parental protein coverage: 72.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VFTTSTVSGGYAEYAVAADHTVYSLPEKLDFKQGAAIGIPYFTAYRALFLSSARAKAGETVLVHGASGGV
          VFTTSTVSG..AEY.VAADH..YSLPE..DFKQGAAIG..YFTAY..L.L.SA...AGE.VLV.GA.G.V
Retrocopy VFTTSTVSGDHAEYVVAADHMIYSLPERMDFKQGAAIGVSYFTAYLVL-LRSAPVRAGEIVLVPGACGRV

Parental  GLAACQIARAYGLKVLGTAGLEKGQNTVLQNGAHKVFNHKDVNYIDEIKKSVGDKGIDVIIEMLANINLS
          GLA.CQIAR.YGLKVLGTAG.EK.QN..LQN.AH..FN.KDV.Y.DEIKKSV.DKG.D.IIEMLA..N.S
Retrocopy GLATCQIARTYGLKVLGTAGTEKSQNIILQNRAHEAFNCKDVSYTDEIKKSVHDKGTDMIIEMLAKVNFS

Parental  NDLKLLSHGGRVIVVGSRGPIEINPRDTMTKES-SIIGVSLFSSSTEEFQQSAAALQAGMETGWLKPVIG
          NDLKLLS.GGRVI.VGSRG.IE.NP..TM.KE...IIGV..FSSS..EFQQ.AAALQAGME.GWLKPVI.
Retrocopy NDLKLLSCGGRVIIVGSRGSIEMNPWETMAKEA>RIIGVAHFSSSLGEFQQFAAALQAGMEIGWLKPVIY

Parental  SQYPLEKVAQAHENIIHGSGTAGKMILLL
          SQYPLEKVAQA.ENII.GS..AGK.I..L
Retrocopy SQYPLEKVAQAQENIIYGSRAAGKIIFPL

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_527 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003162	1 retrocopy	retro_btau_1433,
Canis familiaris	ENSCAFG00000020404	1 retrocopy	retro_cfam_870,
Choloepus hoffmanni	ENSCHOG00000005167	1 retrocopy	retro_chof_1772,
Felis catus	ENSFCAG00000030626	1 retrocopy	retro_fcat_1907,
Homo sapiens	ENSG00000116791	1 retrocopy	retro_hsap_3884,
Loxodonta africana	ENSLAFG00000011371	1 retrocopy	retro_lafr_527 ,
Macaca mulatta	ENSMMUG00000014593	2 retrocopies	retro_mmul_1026, retro_mmul_1728,
Mustela putorius furo	ENSMPUG00000010969	1 retrocopy	retro_mputfur_119,
Mus musculus	ENSMUSG00000028199	1 retrocopy	retro_mmus_1314,
Nomascus leucogenys	ENSNLEG00000009543	2 retrocopies	retro_nleu_1890, retro_nleu_3115,
Otolemur garnettii	ENSOGAG00000011586	1 retrocopy	retro_ogar_179,
Pongo abelii	ENSPPYG00000001235	2 retrocopies	retro_pabe_1909, retro_pabe_3165,
Pan troglodytes	ENSPTRG00000000865	1 retrocopy	retro_ptro_1598,
Tupaia belangeri	ENSTBEG00000016750	3 retrocopies	retro_tbel_1665, retro_tbel_2353, retro_tbel_3800,
Tarsius syrichta	ENSTSYG00000004193	2 retrocopies	retro_tsyr_1218, retro_tsyr_1884,
Tursiops truncatus	ENSTTRG00000010471	2 retrocopies	retro_ttru_555, retro_ttru_958,