RetrogeneDB ID: retro_itri_1126

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393381.1:5307110..5307664(-)
• 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_1126
TCATTTTTGGAGAACATGGAGGTGGAGTGCAACTACCAGTGCTAACACGAGAAAGACCCAGAAAGTTGCTATCAGCTGGT
GGACTATTTCGAAGGGATCCAGAAAAATTTTTATGAGGCTGCCAAGATGTTGAAGTTCAACTGTGAAGAGAACAAGCACA
GTGATAGCTGCTACAAACTGGAGGCCTATTATATGACTGGAAAAGGTGGATGAGCTCAGGACCTGAAAGCTGCCTCGAAC
TGCTTTTGGATGGCATGTGAGAAGCCTGGAAAGAAGTCTGTGGAAGCATGTCACAATGTCGGTCTCCGGGCACATGATGG
CCAGGTCAATGAAGATGGCCAGCCCGACCTGGGAAAGGCCAGGGACTACTACATAAGGGCCTGTAATGGCAACTATGCCT
CCAGTTGCTTCAAGCTTAGTGCCATGTTTCTTTGGCTGCCCCTGGTGTTCCCAAGGATATGGGCCTGGCATGTGAATACC
TGGTGAAAGCCTGTGACCTGGGCCATGGTTGGGCCTGTGTCCATGCTAGCCGCAAGTATAGAATGGAGGATGGT

Alignment

ORF - retro_itri_1126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.1 %
• Parental protein coverage: 80.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFLENMEVECNYQCYHEKDPEGCYRLVDYLEGIQKNFYEAAKVLKFNCEENKHSDSCYKLGAYYVTGKGG
          SFLENMEVECNYQC.HEKDPE.CY.LVDY.EGIQKNFYEAAK.LKFNCEENKHSDSCYKL.AYY.TGKGG
Retrocopy SFLENMEVECNYQC*HEKDPESCYQLVDYFEGIQKNFYEAAKMLKFNCEENKHSDSCYKLEAYYMTGKGG

Parental  LAQDLKAASSCFLMACEKPGKKSVEACHNVGLLAHDGQVNEDGQPDLGKARDYYTRACNGNYASSCFNLS
          .AQDLKAAS.CF.MACEKPGKKSVEACHNVGL.AHDGQVNEDGQPDLGKARDYY.RACNGNYASSCF.LS
Retrocopy *AQDLKAASNCFWMACEKPGKKSVEACHNVGLRAHDGQVNEDGQPDLGKARDYYIRACNGNYASSCFKLS

Parental  AMFL-QGAPGVPKDMGLACEYSMKACDLGHVWACANASRMYKMGDG
          AMFL...APGVPKDMGLACEY..KACDLGH.WAC..ASR.Y.M.DG
Retrocopy AMFL<LAAPGVPKDMGLACEYLVKACDLGHGWACVHASRKYRMEDG

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_1126 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1126 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,