RetrogeneDB ID: retro_itri_1235

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393409.1:3512311..3512532(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1G1
• Ensembl ID: ENSSTOG00000015857
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1 [Source:HGNC Symbol;Acc:864]

Sequence

>retro_itri_1235
GTGACTAGTCGGTCACAGGGGACTCAGCAGCTGCTGCAGGCCGAGAAGGAGGTGGCAGAAGTGTTCAAGGCCAGCAAGTT
GAAGAACACAGGTTGAAGCAGGCCACAGAAACTCGGGCCAACATTAAACAGTGCCACCTGCAGAGGGAGAAAGAGCTCAA
GGCCAAGGAGGTGGTGGCCCTGGGATCCCATGGCAGCTGCAGCTCCAAAGAGGAGAAGGAG

Alignment

ORF - retro_itri_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.94 %
• Parental protein coverage: 64.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASQSQGIQQLLQAEKRAAEKVSEARKRKN-RRLKQAKEEAQAEIEQYRLQREKEFKAKEAAALGSHGSC
          ..S.SQG.QQLLQAEK..AE.V..A.K.KN..RLKQA.E...A.I.Q..LQREKE.KAKE..ALGSHGSC
Retrocopy VTSRSQGTQQLLQAEKEVAE-VFKASKLKN<HRLKQATE-TRANIKQCHLQREKELKAKEVVALGSHGSC

Parental  STEVEKE
          S...EKE
Retrocopy SSKEEKE

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_1235 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1235 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 16 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020461	3 retrocopies	retro_cjac_1788, retro_cjac_2513, retro_cjac_76,
Dasypus novemcinctus	ENSDNOG00000008083	15 retrocopies	retro_dnov_1173, retro_dnov_1447, retro_dnov_1475, retro_dnov_1504, retro_dnov_1588, retro_dnov_1645, retro_dnov_193, retro_dnov_1998, retro_dnov_2179, retro_dnov_218, retro_dnov_2416, retro_dnov_245, retro_dnov_336, retro_dnov_479, retro_dnov_790,
Dipodomys ordii	ENSDORG00000014850	5 retrocopies	retro_dord_434, retro_dord_466, retro_dord_614, retro_dord_640, retro_dord_749,
Echinops telfairi	ENSETEG00000008080	3 retrocopies	retro_etel_350, retro_etel_594, retro_etel_996,
Homo sapiens	ENSG00000136888	3 retrocopies	retro_hsap_3198, retro_hsap_4049, retro_hsap_763,
Gorilla gorilla	ENSGGOG00000004011	4 retrocopies	retro_ggor_1331, retro_ggor_2215, retro_ggor_2717, retro_ggor_632,
Loxodonta africana	ENSLAFG00000013437	2 retrocopies	retro_lafr_1002, retro_lafr_39,
Myotis lucifugus	ENSMLUG00000008657	2 retrocopies	retro_mluc_373, retro_mluc_839,
Macaca mulatta	ENSMMUG00000004899	4 retrocopies	retro_mmul_1783, retro_mmul_2018, retro_mmul_2046, retro_mmul_331,
Monodelphis domestica	ENSMODG00000019574	1 retrocopy	retro_mdom_1675,
Mus musculus	ENSMUSG00000039105	5 retrocopies	retro_mmus_2028, retro_mmus_2784, retro_mmus_2787, retro_mmus_3316, retro_mmus_819,
Nomascus leucogenys	ENSNLEG00000016833	2 retrocopies	retro_nleu_1151, retro_nleu_3045,
Pan troglodytes	ENSPTRG00000021290	2 retrocopies	retro_ptro_2248, retro_ptro_2744,
Ictidomys tridecemlineatus	ENSSTOG00000015857	5 retrocopies	retro_itri_1102, retro_itri_1235 , retro_itri_1281, retro_itri_1340, retro_itri_1669,
Tupaia belangeri	ENSTBEG00000010985	2 retrocopies	retro_tbel_2147, retro_tbel_786,
Tarsius syrichta	ENSTSYG00000011474	3 retrocopies	retro_tsyr_1865, retro_tsyr_2141, retro_tsyr_614,