RetrogeneDB ID: retro_itri_1335

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393445.1:4391734..4392088(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SELRC1
• Ensembl ID: ENSSTOG00000008063
• Aliases: None
• Description: Sel1 repeat containing 1 [Source:HGNC Symbol;Acc:25716]

Sequence

>retro_itri_1335
GGATCCATGGAAGGACTGGACAAGGGGCAGGTAAAGTCATTTTTGGAAAATATTGAGGTGGAGTGCAACTACAAATGCTA
CTGTGAGAAGGACACGGGAGGTTTCTATTGGCTGGTAGACTATTTGGAAGAGGTACAGAAAAATTTTGATGAGACTTCCA
AGGTGCTGAAGTTCAGCTCTGAAGACAATAAGCACAGTGATAACTGCTACAAACTGGAGGCTTATTATATGCTTTGAAAA
CGTGAACTGACTCAGGACCTGAAAGCTGCCTTGAGATGATTTTGGATGGCATGTGATAAACATGGAAAGAAATCTGTGAA
ATTATGTTGCTGTCCTGGCACATTATGGACAGAT

Alignment

ORF - retro_itri_1335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.71 %
• Parental protein coverage: 51.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLVDFQDAEQVKSFLENMEVECNYQCYHEKDPEGCYRLVDYLEGIQKNFYEAAKVLKFNCEENKHSDSCY
          G.....D..QVKSFLEN.EVECNY.CY.EKD..G.Y.LVDYLE..QKNF.E..KVLKF..E.NKHSD.CY
Retrocopy GSMEGLDKGQVKSFLENIEVECNYKCYCEKDTGGFYWLVDYLEEVQKNFDETSKVLKFSSEDNKHSDNCY

Parental  KLGAYYVTGKGGLAQDLKAASSCFLMACEKPGKKSVEACHNVGLLAHD
          KL.AYY...K..L.QDLKAA...F.MAC.K.GKKSV..C...G.L..D
Retrocopy KLEAYYML*KRELTQDLKAALR*FWMACDKHGKKSVKLCCCPGTLWTD

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_1335 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1335 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021584	1 retrocopy	retro_cjac_108,
Ictidomys tridecemlineatus	ENSSTOG00000008063	2 retrocopies	retro_itri_1126, retro_itri_1335 ,