RetrogeneDB ID: retro_itri_398

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:10833831..10834400(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5A
• Ensembl ID: ENSSTOG00000026229
• Aliases: None
• Description: RAB5A, member RAS oncogene family [Source:HGNC Symbol;Acc:9783]

Sequence

>retro_itri_398
ATGGCTAATCGAGGAGTAACAAGCCCGAATAGGCCAAACACTGGAAATAAAATATGCCAGTTCAAACTAGTACTTCTGGG
AGAATATGTGGTTGGCAAATCAAGCCTAGTGCTTCATTTCGTGAAAGGCCAATTTCATGAATTTCAAGAGAGTACTGTTT
GGGTTGCTTTTCTGATCCAAACTGTGTATCTTGAATGACACAACAGTAATATGGGATACAGCTGATGAAGAATGATACCA
CAACCTAGCACCAGTGTACTACAGAGGAACACAAGCAGCCATTGTTGTATAAGATATCACTGAAGAGGAATCCTTTGCAA
GAGCCAAAAACTGGGTTAAAGAACTTCAGAGGCAAGCAAGTCCTAACACTGTAATAATTTTATCAGGAAACAAGGCTGAT
CTAGCAAATAAAAGAACTGTAGATTTCCAGGAAGCACAGTCCTATGCAAATGACAACAGTTTATTATTCATGGAGACATC
AGCTAAAATGTCAATGAATGTAAATGAAATATTCATGGCAATAGCTAAAAAGTTGCCAAAAAAATGAACCACAGAATACC
GGAGCGAGC

Alignment

ORF - retro_itri_398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.51 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MANRGATRPNGPNTGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLD-DTTV
          MANRG.T.PN.PNTGNKICQFKLVLLGE..VGKSSLVL.FVKGQFHEFQEST...AFL.QTV.L..DTTV
Retrocopy MANRGVTSPNRPNTGNKICQFKLVLLGEYVVGKSSLVLHFVKGQFHEFQESTVWVAFLIQTVYLE>DTTV

Parental  KFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLAN
          ...IWDTA..E.YH.LAP.YYRG.QAAIVV.DIT.EESFARAKNWVKELQRQASPN.VI.LSGNKADLAN
Retrocopy ---IWDTADEE*YHNLAPVYYRGTQAAIVV*DITEEESFARAKNWVKELQRQASPNTVIILSGNKADLAN

Parental  KRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP-KNEPQNPGAN
          KR.VDFQEAQSYA.DNSLLFMETSAK.SMNVNEIFMAIAKKLP.KNEPQN.GA.
Retrocopy KRTVDFQEAQSYANDNSLLFMETSAKMSMNVNEIFMAIAKKLP>KNEPQNTGAS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_398 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_398 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398 ,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,