RetrogeneDB ID: retro_itri_1341

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393446.1:2031263..2031731(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2I
• Ensembl ID: ENSSTOG00000010233
• Aliases: None
• Description: SUMO-conjugating enzyme UBC9 [Source:UniProtKB/Swiss-Prot;Acc:Q2EF73]

Sequence

>retro_itri_1341
ATGTCGGGGATCGCCCTCAGCAGACTTGCCCGGGAGAAAAAAGCTTGGAGGAGGGACCATCCCTTTTGCTTGTGGTTGTC
CCAAGTAAGAACCTAGACAGCACGATGAACCTGATGAACTGGGAATGTGCCATCCCAGGAAAGAAGGGGACTCGTGGGAA
GGAGGCTTGTTCAAGCTGTGGATGCTCTTCAAAGATGATCATCCATCCTCACCACCGAAATGTAAATTTGAGCCACCACG
ATTTCACCTGAATGTGTGTCCTTCTGGTATGGAGTGTCTATCCATCCTGGAAGAGGACAAGGACTGGAGGCCAGCCATCA
CGATCAAGCAGATCGTATTAGGAATACGGGAACTTCTAAATGAAACCAAATATGCAAGACCCCACTCAAGCAGAGGCCTA
CATGATTTACTGTGTAAAAACAGAGTGGAATATGAGAAAAGGGTTCAAGCAAGAAGTTTGCACCTTCG

Alignment

ORF - retro_itri_1341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSGIALSRLAQERKAWRKDHPFGF-VAVPTKNPDGTMNLMNWECAIPGKKGT-PWEGGLFKLRMLFKDDY
          MSGIALSRLA.E.KAWR.DHPF...V.VP.KN.D.TMNLMNWECAIPGKKGT..WEGGLFKL.MLFKDD.
Retrocopy MSGIALSRLAREKKAWRRDHPFCL<VVVPSKNLDSTMNLMNWECAIPGKKGT<SWEGGLFKLWMLFKDDH

Parental  PSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNE-PNIQDPAQAEAYTIY
          PSSPPKCKFEPP.FH.NV.PSG..CLSILEEDKDWRPAITIKQI.LGI.ELLNE.PN.QDP.QAEAY.IY
Retrocopy PSSPPKCKFEPPRFHLNVCPSGMECLSILEEDKDWRPAITIKQIVLGIRELLNE>PNMQDPTQAEAYMIY

Parental  CQNRVEYEKR-VRAQA-KKFAPS
          C....E...R..R.QA.KKFAPS
Retrocopy CV-KTEWNMR<KRVQA<KKFAPS

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_1341 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1341 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 18 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007721	1 retrocopy	retro_amel_1843,
Bos taurus	ENSBTAG00000038866	1 retrocopy	retro_btau_1470,
Canis familiaris	ENSCAFG00000031449	4 retrocopies	retro_cfam_1363, retro_cfam_1991, retro_cfam_2090, retro_cfam_541,
Callithrix jacchus	ENSCJAG00000013249	1 retrocopy	retro_cjac_2914,
Cavia porcellus	ENSCPOG00000010431	1 retrocopy	retro_cpor_156,
Equus caballus	ENSECAG00000015831	1 retrocopy	retro_ecab_350,
Felis catus	ENSFCAG00000027291	2 retrocopies	retro_fcat_1994, retro_fcat_873,
Loxodonta africana	ENSLAFG00000018318	1 retrocopy	retro_lafr_541,
Myotis lucifugus	ENSMLUG00000008229	2 retrocopies	retro_mluc_1112, retro_mluc_1327,
Macaca mulatta	ENSMMUG00000003654	1 retrocopy	retro_mmul_981,
Mustela putorius furo	ENSMPUG00000015763	1 retrocopy	retro_mputfur_1234,
Mus musculus	ENSMUSG00000015120	4 retrocopies	retro_mmus_1341, retro_mmus_1997, retro_mmus_3182, retro_mmus_3419,
Nomascus leucogenys	ENSNLEG00000008525	1 retrocopy	retro_nleu_1298,
Otolemur garnettii	ENSOGAG00000001428	4 retrocopies	retro_ogar_2367, retro_ogar_2731, retro_ogar_548, retro_ogar_641,
Rattus norvegicus	ENSRNOG00000017907	11 retrocopies	retro_rnor_1051, retro_rnor_1448, retro_rnor_1764, retro_rnor_1913, retro_rnor_2036, retro_rnor_2147, retro_rnor_2301, retro_rnor_2423, retro_rnor_2927, retro_rnor_708, retro_rnor_832,
Sarcophilus harrisii	ENSSHAG00000007034	1 retrocopy	retro_shar_218,
Sus scrofa	ENSSSCG00000021560	1 retrocopy	retro_sscr_319,
Ictidomys tridecemlineatus	ENSSTOG00000010233	3 retrocopies	retro_itri_1341 , retro_itri_1459, retro_itri_1601,