RetrogeneDB ID: retro_itri_590

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393304.1:12325179..12325544(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1A
• Ensembl ID: ENSSTOG00000012780
• Aliases: None
• Description: SAR1 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10534]

Sequence

>retro_itri_590
GGACTCTTTAAGAAATCTGGAAAAATATTTGTGAGTTTGAACAATGTGGGCAAAGTCAGTCTTTTTCACATGCTCAAAGA
TGACAGATTTACCCAACATATTCTAGCACTACATCTGACATCAGAAGAGCTGATAATAGTGAAATGATATTTATAACTTT
TGATCTTATGGTCATAAGCATGTATGTCGGACGTGGAAAAAATTATCTTCCAGCAATTCATGGGATTGTCTTTCTGATGG
GCTGTGCATATCATTTCCACCCAATGGAATCTAAAGTTGAGATTAATGTTTTAATGAATGACGAAACAATATACAATATA
ATAATATGTATCTTCAGTAACAATATCAGCAGAAAAGATACAATC

Alignment

ORF - retro_itri_590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.32 %
• Parental protein coverage: 62.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTI-AGMTFTTFDL-GGHEQARRVW-
          GL.KKSGK..F..L.N.GK..L.HMLKDDR..QH...LH.TSEEL.I...M.F.TFDL..GH....R.W.
Retrocopy GLFKKSGK-IFVSLNNVGKVSLFHMLKDDRFTQHILALHLTSEELII<SEMIFITFDL<YGHKHVCRTW>

Parental  KNYLPAINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAI
          KNYLPAI.GIVFL..CA.H...MESKVE.N.LM.DETI.N..I.I..N.I.R.D.I
Retrocopy KNYLPAIHGIVFLMGCAYHFHPMESKVEINVLMNDETIYNIIICIFSNNISRKDTI

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_590 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_590 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 13 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016353	5 retrocopies	retro_cjac_1006, retro_cjac_2242, retro_cjac_2305, retro_cjac_4081, retro_cjac_957,
Homo sapiens	ENSG00000079332	4 retrocopies	retro_hsap_2976, retro_hsap_3568, retro_hsap_4714, retro_hsap_639,
Gorilla gorilla	ENSGGOG00000024879	3 retrocopies	retro_ggor_144, retro_ggor_2408, retro_ggor_2929,
Myotis lucifugus	ENSMLUG00000006626	2 retrocopies	retro_mluc_1317, retro_mluc_1996,
Nomascus leucogenys	ENSNLEG00000011243	4 retrocopies	retro_nleu_1987, retro_nleu_2231, retro_nleu_2311, retro_nleu_2759,
Otolemur garnettii	ENSOGAG00000005040	3 retrocopies	retro_ogar_1447, retro_ogar_1981, retro_ogar_2467,
Pongo abelii	ENSPPYG00000002374	4 retrocopies	retro_pabe_2468, retro_pabe_2940, retro_pabe_3661, retro_pabe_565,
Pan troglodytes	ENSPTRG00000002584	4 retrocopies	retro_ptro_2011, retro_ptro_2423, retro_ptro_3133, retro_ptro_465,
Ictidomys tridecemlineatus	ENSSTOG00000011326	1 retrocopy	retro_itri_1714,
Ictidomys tridecemlineatus	ENSSTOG00000012780	2 retrocopies	retro_itri_1191, retro_itri_590 ,
Tupaia belangeri	ENSTBEG00000008657	5 retrocopies	retro_tbel_1060, retro_tbel_14, retro_tbel_2319, retro_tbel_2366, retro_tbel_2846,
Tarsius syrichta	ENSTSYG00000005955	2 retrocopies	retro_tsyr_1204, retro_tsyr_2099,
Vicugna pacos	ENSVPAG00000002631	2 retrocopies	retro_vpac_5, retro_vpac_77,