RetrogeneDB ID: retro_itri_1820

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393902.1:151617..152073(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALG14
• Ensembl ID: ENSSTOG00000025476
• Aliases: None
• Description: ALG14, UDP-N-acetylglucosaminyltransferase subunit [Source:HGNC Symbol;Acc:28287]

Sequence

>retro_itri_1820
ATGGTGTGTTTTCAAATTTTAGCTGCAGCGATCGGAGCTGTGGCTGTGGTCCTAATCCTACGACTATGGATAGTGCTTCG
GCCCCAGGACGTGGCACCCTGGGAGTCCCTCAATCTCCTGGTGGTGGCTGGGTCCGGTGGTCATACCACAGAGATCCTGA
GGCTGGTTGGGAGCTTGTCCAGTGCTTACTCACCTAGACATTATGTCATTGCTGACACTGATGAAATGAGTTCCAATAAA
ATTAAATCTTTTGAACGAGATCAAGCTAATTGAGATTCTAATACCATCTATCCCCAATACTACATTCACCAAATTCCAAG
AAGCCGGGAGGTTCAGCAGTCCTGGTTCTCCACAGTGTTCACCACCTTGCACTCCATGTGGTTCTCCTTTCCTCTGATTC
TCCAAGTAAAGCCAGACTTGGTGTTGTATAATGGACCAGGAACATGTATTCCTATC

Alignment

ORF - retro_itri_1820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.08 %
• Parental protein coverage: 70.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVCFQILAAAIGAVAVVLVLRLWIVLRPQDVVPRESLNLLVVAGSGGHTTEILRLVGSLSSAYSPRHYVI
          MVCFQILAAAIGAVAVVL.LRLWIVLRPQDV.P.ESLNLLVVAGSGGHTTEILRLVGSLSSAYSPRHYVI
Retrocopy MVCFQILAAAIGAVAVVLILRLWIVLRPQDVAPWESLNLLVVAGSGGHTTEILRLVGSLSSAYSPRHYVI

Parental  ADTDEMSSNKIKSFERNQANRDCNTMYPQYYIHQIPRSREVQQSWFSTVFTTLHSMWVSFPLILQVKPDL
          ADTDEMSSNKIKSFER.QAN.D.NT.YPQYYIHQIPRSREVQQSWFSTVFTTLHSMW.SFPLILQVKPDL
Retrocopy ADTDEMSSNKIKSFERDQAN*DSNTIYPQYYIHQIPRSREVQQSWFSTVFTTLHSMWFSFPLILQVKPDL

Parental  VLCNGPGTCIPI
          VL.NGPGTCIPI
Retrocopy VLYNGPGTCIPI

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_1820 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1820 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000008564	1 retrocopy	retro_dord_482,
Procavia capensis	ENSPCAG00000014267	1 retrocopy	retro_pcap_280,
Ictidomys tridecemlineatus	ENSSTOG00000025476	1 retrocopy	retro_itri_1820 ,
Tursiops truncatus	ENSTTRG00000016557	1 retrocopy	retro_ttru_88,