RetrogeneDB ID: retro_itri_954

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393349.1:11705..12231(+)
• Located in intron of: ENSSTOG00000012644

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT1
• Ensembl ID: ENSSTOG00000003311
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1) [Source:HGNC Symbol;Acc:4123]

Sequence

>retro_itri_954
GTGCCAGATCATGTAATTTGAATGGAACAGCACTCTGGATTGATCAGAGCTAGATTGAAAGGAGCTACAGTGTCCAAAGG
CCAGATAATCACCTTCTTAGATGTTCATCACCAGTGCACAGTTAGGTGGTTGGAGCCTCTCTTAGCAAGGATCAAACATG
ACAGGAGAACAGTGATATGTCCTATAATTGACGTGATCACTGATGATACTTTTGAACACATGGCAAGCTCTGATATGACC
TATGGTGGATTCAACTGGAAGCTCAATTTTTGCTGGTATCCTGTTTCCCAGAGAGAAATGGACAGAAGGAAAGATGATTA
GACTCTTCCTGGCAGATCACCTACAATGGCAGGAGGCCTTTTTCCAATTGACAGAGATTACTGTCAGGAAATTGGAACAT
ATGATGCTAGAATGCATATTTGGAGAGGAGGAAAAACTAGAAATTTCCTTTAAGATTTGGCAATGTGGAGGAATTTTGGA
AATTGTCACTTGCTCACATGTTGAACACGTGTTTTGGAAAGCTACC

Alignment

ORF - retro_itri_954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.95 %
• Parental protein coverage: 51.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPVHVIRMEQRSGLIRARLKGAAVSKGQVITFLDAHCECTVGWLEPLLARIKHDRRTVVCPIIDVISDDT
          VP.HVI.MEQ.SGLIRARLKGA.VSKGQ.ITFLD.H..CTV.WLEPLLARIKHDRRTV.CPIIDVI.DDT
Retrocopy VPDHVI*MEQHSGLIRARLKGATVSKGQIITFLDVHHQCTVRWLEPLLARIKHDRRTVICPIIDVITDDT

Parental  FEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKGDRTLPVRTPTMAGGLFSIDRDYFQEIGTYDAGMDI
          FE.MA.SDMTYGGFNWKLNF.WYPV.QREMDRRK.D.TLP.R.PTMAGGLF.IDRDY.QEIGTYDA.M.I
Retrocopy FEHMASSDMTYGGFNWKLNFCWYPVSQREMDRRKDD*TLPGRSPTMAGGLFPIDRDYCQEIGTYDARMHI

Parental  WGG-ENLEISFRIWQCGGTLEIVTCSHVGHVFRKAT
          W.G.E.LEISF.IWQCGG.LEIVTCSHV.HVF.KAT
Retrocopy WRG>EKLEISFKIWQCGGILEIVTCSHVEHVFWKAT

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_954 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_954 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011206	1 retrocopy	retro_btau_581,
Callithrix jacchus	ENSCJAG00000021030	2 retrocopies	retro_cjac_1554, retro_cjac_865,
Myotis lucifugus	ENSMLUG00000001978	1 retrocopy	retro_mluc_163,
Mus musculus	ENSMUSG00000000420	1 retrocopy	retro_mmus_1312,
Ictidomys tridecemlineatus	ENSSTOG00000003311	1 retrocopy	retro_itri_954 ,
Ictidomys tridecemlineatus	ENSSTOG00000021306	1 retrocopy	retro_itri_41,
Tarsius syrichta	ENSTSYG00000014610	1 retrocopy	retro_tsyr_1444,