RetrogeneDB ID: retro_lafr_839

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:50856025..50856655(-)
• Located in intron of: ENSLAFG00000016335

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP23
• Ensembl ID: ENSLAFG00000005462
• Aliases: None
• Description: Synaptosomal-associated protein [Source:UniProtKB/TrEMBL;Acc:G3SWA1]

Sequence

>retro_lafr_839
ATGGATAATCTGTCATCAGGAGAAATTCAGCTGAGGGCTCACCAGGTTACTGATGAGTCTCTGGAAAGTACAAGGAGAAT
CCTGGGTTTGGCCATTGAGTCTCAGGATGCAGGAATCAAGACCATCACCATGCTGGATGAACAAGGGGAACAACTAAACC
GTATAGGAGAAGACATGGACCAAATCAAAAAAGACATGAGAGAGGCAGAGAAGACTTTAACAGAACTCGACAAGTGCTGT
GGTCTTTGTGTCTGCCCATGTAACAAGGTGAAGAACTTTGAGTCTGGTGAGGCCTCTAAGGCAACATGGGGAGATGGCGG
AGACAACTCACCTAATGTAATATCTAAGCAGCCAGGCCGGGCGGCAAATGGCCAGCCTCTGCAAGCAGGCACAGGAGCAG
CCAGCAGTGGATACATTAAACGTGTAACTAATGATGCCAGAGAAGATGAAATGGAGGAGAACTTGACTCAGGTGGGCAGC
ATCCTGGGAAATCTAAAAAACATGGCCCTGGACATGGGCAATGAGATTGAGGCTCAAAATCGACAGATAGACCGGATCAC
AGAAAAGGCTGACAGCAACAAAGATCGTATTGACATTGCCAATGCCAGAGCAAAGAAACTCATTGACAGC

Alignment

ORF - retro_lafr_839 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDNLSPEEIQLRAQQVTDESLESTRRILGLAIESQDAGVKTMGMLAEQGEQLKRVEEGMNQINEDMKEAE
          MDNLS..EIQLRA.QVTDESLESTRRILGLAIESQDAG.KT..ML.EQGEQL.R..E.M.QI..DM.EAE
Retrocopy MDNLSSGEIQLRAHQVTDESLESTRRILGLAIESQDAGIKTITMLDEQGEQLNRIGEDMDQIKKDMREAE

Parental  KTLTELNKCCGLCVCPCNRTKNFESSKAYKTTWGDGRDNSDNNVVSKQPGRVTNGQPQQAAKGAASGGYI
          KTLTEL.KCCGLCVCPCN..KNFES..A.K.TWGDG.DNS..NV.SKQPGR..NGQP.QA..GAAS.GYI
Retrocopy KTLTELDKCCGLCVCPCNKVKNFESGEASKATWGDGGDNSP-NVISKQPGRAANGQPLQAGTGAASSGYI

Parental  KRITNDAREDEMEENLTQVGSILGNLKNMALDMGNEIDAHNRQIERITEKADTNKDRIDNANARAKKLID
          KR.TNDAREDEMEENLTQVGSILGNLKNMALDMGNEI.A.NRQI.RITEKAD.NKDRID.ANARAKKLID
Retrocopy KRVTNDAREDEMEENLTQVGSILGNLKNMALDMGNEIEAQNRQIDRITEKADSNKDRIDIANARAKKLID

Parental  S
          S
Retrocopy S

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_839 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839 ,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,