RetrogeneDB ID: retro_itri_449

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393292.1:7021667..7022071(-)
• Located in intron of: ENSSTOG00000002096

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000024226
• Aliases: None
• Description: None

Sequence

>retro_itri_449
ATGGCTTGTACAAAGCGAAATGCCAGCAAATCAAGGGTTGCTAAAGCACTCAGGAAACAACTGGCTGCAAAAGCCGCTTG
CAAGAGTGCGCCCTCTACTGGAGGGGTGAAGAACCCTCACTGTTACAGGCCTGGTACTGTGGCAGTCCGTGAAATTAGAT
GGTATTAGAAGTCCATTGAACTTCTGATGCGCAAACTCCCCTTCCAGCATCTGGTGCTAGAAATTGCTCAGGACTTCAAA
ACAGAGATGCACTTCCAGAGCGCAGCTATTGGTGCTTTGCAGGAGTCAAGTTAGGCCTATCTGGTTGGCCTTTTTGAAGA
CACCAACCTGTGTGTTATCCATGCCAAACGTGTAACAATTATACCAAAAACATCCAACTATCATGCTGCATACATAGAGA
ACGT

Alignment

ORF - retro_itri_449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.74 %
• Parental protein coverage: 99.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MA.TK..A.KS...KA.RKQLA.KAA.KSAPSTGGVK.PH.YRPGTVA.REIR.Y.KS.ELL.RKLPFQ.
Retrocopy MACTKRNASKSRVAKALRKQLAAKAACKSAPSTGGVKNPHCYRPGTVAVREIRWY*KSIELLMRKLPFQH

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMP-KDIQLARRIRGER
          LV.EIAQDFKT...FQSAAIGALQE.S.AYLVGLFEDTNLC.IHAKRVTI.P.K.IQL...I..ER
Retrocopy LVLEIAQDFKTEMHFQSAAIGALQESS*AYLVGLFEDTNLCVIHAKRVTIIP<KNIQLSCCIHRER

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_449 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_449 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 14 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009765	3 retrocopies	retro_amel_1636, retro_amel_1794, retro_amel_192,
Choloepus hoffmanni	ENSCHOG00000009661	10 retrocopies	retro_chof_1580, retro_chof_1635, retro_chof_1911, retro_chof_2281, retro_chof_2294, retro_chof_2343, retro_chof_2546, retro_chof_454, retro_chof_517, retro_chof_530,
Cavia porcellus	ENSCPOG00000004707	7 retrocopies	retro_cpor_1059, retro_cpor_1390, retro_cpor_1524, retro_cpor_432, retro_cpor_695, retro_cpor_842, retro_cpor_853,
Gorilla gorilla	ENSGGOG00000022928	7 retrocopies	retro_ggor_1964, retro_ggor_2181, retro_ggor_2198, retro_ggor_2357, retro_ggor_2805, retro_ggor_2905, retro_ggor_2987,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Myotis lucifugus	ENSMLUG00000015447	10 retrocopies	retro_mluc_146, retro_mluc_1571, retro_mluc_2286, retro_mluc_2344, retro_mluc_2364, retro_mluc_246, retro_mluc_2468, retro_mluc_2500, retro_mluc_392, retro_mluc_613,
Mus musculus	ENSMUSG00000060743	19 retrocopies	retro_mmus_1053, retro_mmus_1116, retro_mmus_1139, retro_mmus_1151, retro_mmus_1254, retro_mmus_2285, retro_mmus_2614, retro_mmus_2934, retro_mmus_3009, retro_mmus_3213, retro_mmus_3425, retro_mmus_395, retro_mmus_498, retro_mmus_808, retro_mmus_884, retro_mmus_885, retro_mmus_886, retro_mmus_959, retro_mmus_960,
Oryctolagus cuniculus	ENSOCUG00000024644	2 retrocopies	retro_ocun_185, retro_ocun_217,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Ochotona princeps	ENSOPRG00000015952	2 retrocopies	retro_opri_1180, retro_opri_937,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Ictidomys tridecemlineatus	ENSSTOG00000024226	8 retrocopies	retro_itri_315, retro_itri_449 , retro_itri_465, retro_itri_505, retro_itri_649, retro_itri_695, retro_itri_764, retro_itri_771,
Tupaia belangeri	ENSTBEG00000006177	13 retrocopies	retro_tbel_110, retro_tbel_1274, retro_tbel_15, retro_tbel_170, retro_tbel_2335, retro_tbel_3341, retro_tbel_3342, retro_tbel_3820, retro_tbel_391, retro_tbel_487, retro_tbel_592, retro_tbel_783, retro_tbel_978,
Vicugna pacos	ENSVPAG00000011531	5 retrocopies	retro_vpac_107, retro_vpac_637, retro_vpac_646, retro_vpac_76, retro_vpac_96,