RetrogeneDB ID: retro_itri_510

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393297.1:4429685..4430067(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC2
• Ensembl ID: ENSSTOG00000023766
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) [Source:HGNC Symbol;Acc:9802]

Sequence

>retro_itri_510
ATGTAAGCCATCAAGAGTGTGGTGGTGGGAGAGGAGCTATAGGTAAAATCTCCCTACTGATCAGCTGTACAACCAATGCA
TTTCCCAGAGAGTATATCCCCACTGTCTTTGACAACTGATCTGCCAATTTCATGGCAGAGAGGAAACCGATGAATCCAGG
CTTATGGGATACAGCTGGAGAAGAAGCTTTTGACAGATTGAACCCTCTCTTCTATCCACAAACAGATGTTTTCTTAATTT
TCTTTTCCCTTGTGAGTCCTGCATCATTTGACATTGTCCATGCAAACTGGTATCTAGAGTTATGACTCCATGTCCCAACA
CTCTTATCATCCTAGTGGGAACACAACTTGATCTTAGGGATAATAACTACATGATTAAGAAA

Alignment

ORF - retro_itri_510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQAIKCVVVGD-GAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDSKPVNLGLWDTAGQEDYDRLRP
          M.AIK.VVVG..GA.GK..LLIS.TTNAFP.EYIPTVFDN.SAN.M...KP.N.GLWDTAG.E..DRL.P
Retrocopy M*AIKSVVVGE<GAIGKISLLISCTTNAFPREYIPTVFDN*SANFMAERKPMNPGLWDTAGEEAFDRLNP

Parental  LSYPQTDVFLICFSLVSPASYENVRAKWFPEVRHH-CPSTPIILVGTKLDLRDDKDTIER
          L.YPQTDVFLI.FSLVSPAS...V.A.W..E...H.CP.T.IILVGT.LDLRD....I..
Retrocopy LFYPQTDVFLIFFSLVSPASFDIVHANWYLEL*LH<CPNTLIILVGTQLDLRDNNYMIKK

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_510 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_510 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 23 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009889	2 retrocopies	retro_amel_1691, retro_amel_647,
Callithrix jacchus	ENSCJAG00000002144	4 retrocopies	retro_cjac_1158, retro_cjac_1954, retro_cjac_2917, retro_cjac_847,
Equus caballus	ENSECAG00000022570	2 retrocopies	retro_ecab_619, retro_ecab_705,
Erinaceus europaeus	ENSEEUG00000009509	1 retrocopy	retro_eeur_20,
Felis catus	ENSFCAG00000025776	2 retrocopies	retro_fcat_1064, retro_fcat_826,
Gorilla gorilla	ENSGGOG00000010612	2 retrocopies	retro_ggor_1403, retro_ggor_188,
Loxodonta africana	ENSLAFG00000013012	1 retrocopy	retro_lafr_117,
Macropus eugenii	ENSMEUG00000012295	2 retrocopies	retro_meug_252, retro_meug_552,
Microcebus murinus	ENSMICG00000017775	4 retrocopies	retro_mmur_1104, retro_mmur_1557, retro_mmur_20, retro_mmur_600,
Myotis lucifugus	ENSMLUG00000012668	2 retrocopies	retro_mluc_326, retro_mluc_860,
Macaca mulatta	ENSMMUG00000018854	2 retrocopies	retro_mmul_1346, retro_mmul_210,
Mustela putorius furo	ENSMPUG00000012682	2 retrocopies	retro_mputfur_872, retro_mputfur_911,
Nomascus leucogenys	ENSNLEG00000014759	7 retrocopies	retro_nleu_1215, retro_nleu_1330, retro_nleu_2094, retro_nleu_2355, retro_nleu_689, retro_nleu_724, retro_nleu_87,
Oryctolagus cuniculus	ENSOCUG00000016115	1 retrocopy	retro_ocun_43,
Otolemur garnettii	ENSOGAG00000004138	1 retrocopy	retro_ogar_2977,
Pongo abelii	ENSPPYG00000011791	3 retrocopies	retro_pabe_1591, retro_pabe_21, retro_pabe_3818,
Pteropus vampyrus	ENSPVAG00000002281	2 retrocopies	retro_pvam_21, retro_pvam_609,
Sarcophilus harrisii	ENSSHAG00000014852	1 retrocopy	retro_shar_763,
Sus scrofa	ENSSSCG00000021944	4 retrocopies	retro_sscr_40, retro_sscr_565, retro_sscr_582, retro_sscr_882,
Ictidomys tridecemlineatus	ENSSTOG00000000805	4 retrocopies	retro_itri_1158, retro_itri_1602, retro_itri_1615, retro_itri_431,
Ictidomys tridecemlineatus	ENSSTOG00000006784	1 retrocopy	retro_itri_1503,
Ictidomys tridecemlineatus	ENSSTOG00000023766	1 retrocopy	retro_itri_510 ,
Tursiops truncatus	ENSTTRG00000001099	8 retrocopies	retro_ttru_1029, retro_ttru_1065, retro_ttru_1188, retro_ttru_1599, retro_ttru_1904, retro_ttru_318, retro_ttru_379, retro_ttru_825,