RetrogeneDB ID: retro_itri_1193

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393397.1:4501995..4502219(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSSTOG00000025405
• Aliases: None
• Description: small ubiquitin-like modifier 1 [Source:HGNC Symbol;Acc:12502]

Sequence

>retro_itri_1193
ATGTCTGACCAGGGGACAAAACCTTCAACTGAGGATTTGAGGGATAAGAAAGGAGAATATATTTAGACTCAAAGTCAATA
TACATGATTGCAGTGAGATCACTTCAAAGTGAAATGACAACACATCTCAAGAAACTCAAAGAACCATACTATCAAAGACA
GGAGGTTCCAATGAATTCACTCAGGTTTCTCTTTGAAGATCAGAGAATTGCTGATAATCATACT

Alignment

ORF - retro_itri_1193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.75 %
• Parental protein coverage: 75.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSDQEAKPSTEDLGDKKEGEYI-KLKVIGQDSSEI-HFKVK-MTTHLKKLKESYCQRQGVPMNSLRFLFE
          MSDQ..KPSTEDL.DKK.GEYI..LKV...D.SEI.HFKVK.MTTHLKKLKE.Y.QRQ.VPMNSLRFLFE
Retrocopy MSDQGTKPSTEDLRDKK-GEYI>RLKVNIHDCSEI<HFKVK<MTTHLKKLKEPYYQRQEVPMNSLRFLFE

Parental  GQRIADNHT
          .QRIADNHT
Retrocopy DQRIADNHT

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_1193 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1193 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 20 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Callithrix jacchus	ENSCJAG00000004961	3 retrocopies	retro_cjac_1686, retro_cjac_1932, retro_cjac_2610,
Cavia porcellus	ENSCPOG00000012143	1 retrocopy	retro_cpor_1279,
Equus caballus	ENSECAG00000024693	4 retrocopies	retro_ecab_199, retro_ecab_365, retro_ecab_570, retro_ecab_935,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Homo sapiens	ENSG00000116030	5 retrocopies	retro_hsap_2007, retro_hsap_240, retro_hsap_2489, retro_hsap_262, retro_hsap_897,
Gorilla gorilla	ENSGGOG00000026439	5 retrocopies	retro_ggor_1451, retro_ggor_1550, retro_ggor_299, retro_ggor_311, retro_ggor_725,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Mustela putorius furo	ENSMPUG00000000335	2 retrocopies	retro_mputfur_257, retro_mputfur_33,
Mus musculus	ENSMUSG00000026021	5 retrocopies	retro_mmus_1594, retro_mmus_2129, retro_mmus_2135, retro_mmus_252, retro_mmus_2962,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Rattus norvegicus	ENSRNOG00000016133	2 retrocopies	retro_rnor_2015, retro_rnor_813,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,
Ictidomys tridecemlineatus	ENSSTOG00000010587	2 retrocopies	retro_itri_116, retro_itri_1259,
Ictidomys tridecemlineatus	ENSSTOG00000024685	10 retrocopies	retro_itri_1017, retro_itri_1123, retro_itri_1355, retro_itri_202, retro_itri_264, retro_itri_272, retro_itri_79, retro_itri_921, retro_itri_981, retro_itri_983,
Ictidomys tridecemlineatus	ENSSTOG00000025405	4 retrocopies	retro_itri_1193 , retro_itri_1232, retro_itri_216, retro_itri_668,
Tursiops truncatus	ENSTTRG00000000642	4 retrocopies	retro_ttru_1646, retro_ttru_1652, retro_ttru_309, retro_ttru_399,