RetrogeneDB ID: retro_itri_1835

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393973.1:45456..46136(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM120A
• Ensembl ID: ENSSTOG00000021804
• Aliases: None
• Description: family with sequence similarity 120A [Source:HGNC Symbol;Acc:13247]

Sequence

>retro_itri_1835
CCACCAGAATTCTCACTAGTGATCATGAAGGAATGGGCAGCTTACAAGGGGCAATCTCCTCCAACCAAGTCTCAGGGCAG
GGGCAGAGGCTTTGCAGGAGTCTGTGGCTTTGGCAGCCCTTATGGGAAAACCATAGCAACTGGCCCTTACCATGCCTTCT
GGGTGGAGGCAGCATCAGAACACTGTGGAGCCTTCTTAGGCACTGACAGCAGTGAAACTAGCAAGTCCCAGGGTGGAGTC
CAAACTATACCTTCTCAGGGAGGGAAACTAGAAATCGCTGGCACTGTGGTTGGACACTGGGCAGGAAGCAGGCAGGGCTG
TGGAGTCTGAGGGCCCTTCCCATTGCAAGTGGTCTCTGTCGGAGGAACAACAAGAGGGCATCCAATAGGAGTTATTTCCA
TCCTAGAAATACAGAGGTTTGGTAGAGTTGGAAGGCACTATGGCCGAGGTTGTAAAAGCCAGGGAGCAATTCAGGGCAGA
CCTCCTTATGCTGCTTCAGAGGAAGAAGTGGCCAAAGAGCTGAAGTCAAAATCTGGGGAATCAAAGTCCTTTGCCATGTC
TTCACACGGGTCCCTGCCTGAAAATGCAGTGATGGCCGAGGAAAAGCCAGTACCCCAGATGAATGAAAGTGCAGGGGACA
CCAGGGCCCCCAGCCACTCAAAAGTGCCTTGAACAATGAC

Alignment

ORF - retro_itri_1835 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.88 %
• Parental protein coverage: 55.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPALPFYPASVYPRHFGPVPP--SQGRGRGFAGVCGFGGPYGETVASGPYRAFRVAAASGHCGAFSGSDS
          PP..............G..PP..SQGRGRGFAGVCGFG.PYG.T.A.GPY.AF.V.AAS.HCGAF.G.DS
Retrocopy PPEFSLVIMKEWAAYKGQSPPTKSQGRGRGFAGVCGFGSPYGKTIATGPYHAFWVEAASEHCGAFLGTDS

Parental  SRTSKSQGGVQPIPSQGGKLEIAGTVVGHWAGSRRGRGGRGPFPLQVVSVGGPARGRPRGVISTPVIRTF
          S.TSKSQGGVQ.IPSQGGKLEIAGTVVGHWAGSR.G.G..GPFPLQVVSVGG..RG.P.GVIS...I..F
Retrocopy SETSKSQGGVQTIPSQGGKLEIAGTVVGHWAGSRQGCGV*GPFPLQVVSVGGTTRGHPIGVISILEIQRF

Parental  GRGGRYYGRGYKSQGAIQGRPPYAASAEEVAKELKSKSGESKSSAVSSDGSLAENGVMAEEKPVPQMNGS
          GR.GR.YGRG.KSQGAIQGRPPYAAS.EEVAKELKSKSGESKS.A.SS.GSL.EN.VMAEEKPVPQMN.S
Retrocopy GRVGRHYGRGCKSQGAIQGRPPYAASEEEVAKELKSKSGESKSFAMSSHGSLPENAVMAEEKPVPQMNES

Parental  AGDTRAPSHS-ESALNND
          AGDTRAPSHS..SALNND
Retrocopy AGDTRAPSHS<KSALNND

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_1835 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1835 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000021804	2 retrocopies	retro_itri_1835 , retro_itri_1883,