RetrogeneDB ID: retro_itri_951

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393348.1:7796696..7797489(+)
• Located in intron of: ENSSTOG00000005128

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000026103
• Aliases: None
• Description: None

Sequence

>retro_itri_951
ATGGCTTCAGATTTTGCCTTCTCGCCCCCTCTGGGAGGTGGGGGTGATGGGTCAGGAGGGCCAGAGCCGAGCCGGATTGA
CCCTCAGACCTGGCTAAGCTTCCCAGGCCCTCCCGGTGGTCCAGGAATCGGGCCAGGTTCGGAGGTGTGGGGGATTCCCT
CATTGCCCTCTGCCCTATGAGTTCTGTGGAGAGATGGCATACTGTGGACCTCAGGTTGGAATGGGCCTGATCCCCCATGG
TAGCCTGGAGAGCTCTCAGCCTGAGATGGAGGGGGAGCTGGGATGGAAAGCAACTCTGAAGGGGCCTCCCCCGAGCCCTG
CATTGCTCACCCTGCTGTGGTGAAAGTGGAGAGGAAAAGGTGGATTAAAACCCTGAGGAATCCCAAGATATCCAAGCTTG
GCAGAAAGAATTGGAGAAATTTGCCAAGCTACTGAAGCAGAAGAGGATCAACCTGGGATATACTCAGGCCGATGTGGGGC
TCACACTGGGGTTCTCTTTGGGAAGGTGTTCAGCCAAACGACCACCTGCCGTTTTGAGGCTCTGCAGCTTAGTTTCAAGA
ACATGTGCAAGCTGCGGCCCATGCTACAGAAGTGGGTGGAGGAAGCAGACAATAATAAAAACCTTCAGAAGATATGCAAA
GCAGAGACCCTCCTGCAAGCCCGGAAGAGAAAGCGAACAAATATTGAGACCGGAGTGAGAGGCAACCTGGAGAAGATGTT
CTTGCAATACCCAAAATCCATACTGCAGGAGATCAGCCACACTGCCGAACACCTAGAGCTTAAGAAGGATGTG

Alignment

ORF - retro_itri_951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.78 %
• Parental protein coverage: 74.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LASDFAFSPPPGGGGDGPGGPEPGWIDHRTWLSFPGPPGGPVIGPGVGPGSEVWGIPSYPP-PHEFCGGM
          .ASDFAFSPP.GGGGDG.GGPEP..ID..TWLSFPGPPG....GPG.GPGSEVWGIPS.P..P.EFCG.M
Retrocopy MASDFAFSPPLGGGGDGSGGPEPSRIDPQTWLSFPGPPG----GPGIGPGSEVWGIPSLPS>PYEFCGEM

Parental  AYCGPQVGKGLIPHGGLETSQPEVEV-GAGMESNSEGASPEPCIAHPAVVKVEK-EKMDQNPEESQDIQA
          AYCGPQVG.GLIPHG.LE.SQPE.E..GAGMESNSEGASPEPCIAHPAVVKVE..EK.D.NPEESQDIQA
Retrocopy AYCGPQVGMGLIPHGSLESSQPEMEG<GAGMESNSEGASPEPCIAHPAVVKVER<EKVD*NPEESQDIQA

Parental  LQKELEEFAKLLKQKRINLGYTQADVGLTLG-VLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVEE
          .QKELE.FAKLLKQKRINLGYTQADVGLTLG.VLFGKVFSQTT.CRFEALQLSFKNMCKLRP.LQKWVEE
Retrocopy WQKELEKFAKLLKQKRINLGYTQADVGLTLG<VLFGKVFSQTTTCRFEALQLSFKNMCKLRPMLQKWVEE

Parental  ADNNENLQEICKAEALLQARKRKRTSIENRVRGNLENMFLQCPKPTLQQISHIAEQLGLEKDV
          ADNN.NLQ.ICKAE.LLQARKRKRT.IE..VRGNLE.MFLQ.PK..LQ.ISH.AE.L.L.KDV
Retrocopy ADNNKNLQKICKAETLLQARKRKRTNIETGVRGNLEKMFLQYPKSILQEISHTAEHLELKKDV

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_951 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_951 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 29 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010377	3 retrocopies	retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus	ENSBTAG00000021111	2 retrocopies	retro_btau_1576, retro_btau_951,
Canis familiaris	ENSCAFG00000000485	1 retrocopy	retro_cfam_1538,
Callithrix jacchus	ENSCJAG00000019789	1 retrocopy	retro_cjac_123,
Dasypus novemcinctus	ENSDNOG00000003949	1 retrocopy	retro_dnov_2267,
Dipodomys ordii	ENSDORG00000009549	1 retrocopy	retro_dord_65,
Equus caballus	ENSECAG00000008967	1 retrocopy	retro_ecab_301,
Erinaceus europaeus	ENSEEUG00000015357	2 retrocopies	retro_eeur_196, retro_eeur_558,
Felis catus	ENSFCAG00000001078	3 retrocopies	retro_fcat_1372, retro_fcat_1422, retro_fcat_275,
Gallus gallus	ENSGALG00000026574	1 retrocopy	retro_ggal_18,
Gorilla gorilla	ENSGGOG00000027662	3 retrocopies	retro_ggor_2275, retro_ggor_295, retro_ggor_852,
Macropus eugenii	ENSMEUG00000013221	3 retrocopies	retro_meug_1146, retro_meug_1475, retro_meug_692,
Meleagris gallopavo	ENSMGAG00000000739	1 retrocopy	retro_mgal_8,
Microcebus murinus	ENSMICG00000001511	1 retrocopy	retro_mmur_1423,
Myotis lucifugus	ENSMLUG00000011028	3 retrocopies	retro_mluc_1465, retro_mluc_2382, retro_mluc_515,
Mustela putorius furo	ENSMPUG00000001202	2 retrocopies	retro_mputfur_253, retro_mputfur_96,
Mus musculus	ENSMUSG00000024406	2 retrocopies	retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus	ENSOCUG00000017160	3 retrocopies	retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Otolemur garnettii	ENSOGAG00000000621	3 retrocopies	retro_ogar_1406, retro_ogar_1436, retro_ogar_2229,
Ochotona princeps	ENSOPRG00000003926	2 retrocopies	retro_opri_1213, retro_opri_556,
Pongo abelii	ENSPPYG00000017210	3 retrocopies	retro_pabe_2761, retro_pabe_3294, retro_pabe_898,
Pan troglodytes	ENSPTRG00000017953	5 retrocopies	retro_ptro_1798, retro_ptro_204, retro_ptro_2132, retro_ptro_2721, retro_ptro_733,
Pteropus vampyrus	ENSPVAG00000007334	2 retrocopies	retro_pvam_724, retro_pvam_74,
Rattus norvegicus	ENSRNOG00000046487	4 retrocopies	retro_rnor_1474, retro_rnor_2186, retro_rnor_2968, retro_rnor_921,
Sus scrofa	ENSSSCG00000001393	2 retrocopies	retro_sscr_252, retro_sscr_678,
Ictidomys tridecemlineatus	ENSSTOG00000026103	3 retrocopies	retro_itri_1076, retro_itri_1705, retro_itri_951 ,
Tupaia belangeri	ENSTBEG00000013044	4 retrocopies	retro_tbel_3628, retro_tbel_3718, retro_tbel_3779, retro_tbel_4614,
Taeniopygia guttata	ENSTGUG00000002412	1 retrocopy	retro_tgut_25,
Tarsius syrichta	ENSTSYG00000007340	4 retrocopies	retro_tsyr_1508, retro_tsyr_1630, retro_tsyr_814, retro_tsyr_817,