RetrogeneDB ID: retro_itri_1825

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393917.1:210374..210887(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC14A
• Ensembl ID: ENSSTOG00000027626
• Aliases: None
• Description: cell division cycle 14A [Source:HGNC Symbol;Acc:1718]

Sequence

>retro_itri_1825
ATGCAGTATGGCTCCTTAAATTTCAACACATTTGACCTTGAGGAGTACGAACACTACGAAAGAGCAGAAAATGGAGATTT
AAACTGGATAATACCAGACCGCTTCGTTGCCTTCCGTGGGCCTCACGCAAGATCCAGACTTGAAAGTGGTTATCACCAAC
ATTCTCCTGAGACTTACATTCCATATTTTAAGACTCACAATGTCACTACCATTATTCGTCTGGATAAAAGGATGTATGAT
GCCAAGCGCTTCACGGATGCTGGGTTTGATCACCACGATCTTTTCTTTGCGGACGGCAGCACCCCACCCGATGCCATTGT
CAAAGAGTTTCTGGATATTTGTGGGAATGCCGAGGGTGCCATGGCCGTGCACTGTAAAGCCGGCCTCGGTCGCACAGGCA
CTCTGATAGCCTGCTACATCATGAAGCACTACAGGATGACAGCCGCCGAGACCATCGCGTGGGTCCGCATCTGTAGACCC
GGCTCTGTGATTGGGCCCCAGCAGCAGTTCTTG

Alignment

ORF - retro_itri_1825 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.76 %
• Parental protein coverage: 86.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQHGFFDFETFDVEEYEHYERVENGDFNWIVPGKFLAFSGPHPKSKIENGYPLHAPEAYFPYFKKHNVTA
          .Q.G...F.TFD.EEYEHYER.ENGD.NWI.P..F.AF.GPH..S..E.GY..H.PE.Y.PYFK.HNVT.
Retrocopy MQYGSLNFNTFDLEEYEHYERAENGDLNWIIPDRFVAFRGPHARSRLESGYHQHSPETYIPYFKTHNVTT

Parental  VVRLNKKIYEAKRFTDAGFEHYDLFFIDGSTPSDNIVRRFLNICENTEGAIAVHCKAGLGRTGTLIACYV
          ..RL.K..Y.AKRFTDAGF.H.DLFF.DGSTP.D.IV..FL.IC.N.EGA.AVHCKAGLGRTGTLIACY.
Retrocopy IIRLDKRMYDAKRFTDAGFDHHDLFFADGSTPPDAIVKEFLDICGNAEGAMAVHCKAGLGRTGTLIACYI

Parental  MKHYRFTHAEIIAWIRICRPGSIIGPQQHFL
          MKHYR.T.AE.IAW.RICRPGS.IGPQQ.FL
Retrocopy MKHYRMTAAETIAWVRICRPGSVIGPQQQFL

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_1825 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1825 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000012205	1 retrocopy	retro_itri_1799,
Ictidomys tridecemlineatus	ENSSTOG00000027626	1 retrocopy	retro_itri_1825 ,
Ictidomys tridecemlineatus	ENSSTOG00000028527	3 retrocopies	retro_itri_1798, retro_itri_1821, retro_itri_1890,