RetrogeneDB ID: retro_itri_1426

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393483.1:1278371..1278779(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HLA-DOB
• Ensembl ID: ENSSTOG00000003405
• Aliases: None
• Description: major histocompatibility complex, class II, DO beta [Source:HGNC Symbol;Acc:4937]

Sequence

>retro_itri_1426
CTGCATCAGCACAACCTCTGCTCCATGACAGGCTTCTATCCAGGGGACATAAAGACCAGGTGGTTCTGGAATGGACAGGA
GGAGAGAGCTGGCATTATGTCCACTGGTCTTATTAGGAATGGAGACTGGACCTTTCAGACCATAGTGATGCTGGAAGCGA
CTCCTTCATCTGGAGATGTTTACAGCTGTCTTGTTGAGCACCCCAGTCTGTTGAGCCCTGTTTCTGTGGAGTGGAGAGAT
CAGTATGAATATTCTTGGAAAAAGATACCAAATGGAGTTGGAGCCTTCCTGCTTGGGCTAATTGTCCTTATGGTGGGGAT
TGTCATCCACCTCAGGGCTAGGAAAGGATCTGTGGAGACTCAGTCTGGTGATGAGGTCTCAAGAGCTATTCCACAGCAGC
CATACTCA

Alignment

ORF - retro_itri_1426 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 50.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHQHNLLLCSVTGFYPGDIKIRWFWNGQEERAGVLSTGLIRNGDWTFQTMVMLEVTPSPGDVYSCLVEHP
          LHQHNL..CS.TGFYPGDIK.RWFWNGQEERAG..STGLIRNGDWTFQT.VMLE.TPS.GDVYSCLVEHP
Retrocopy LHQHNL--CSMTGFYPGDIKTRWFWNGQEERAGIMSTGLIRNGDWTFQTIVMLEATPSSGDVYSCLVEHP

Parental  SLPGPVSVEWRAQREYSWKKILSGVGAFLLGLTFLLVGIIIHLRARKGSVETQSGDKISRAILQKPNS
          SL..PVSVEWR.Q.EYSWKKI..GVGAFLLGL..L.VGI.IHLRARKGSVETQSGD..SRAI.Q.P.S
Retrocopy SLLSPVSVEWRDQYEYSWKKIPNGVGAFLLGLIVLMVGIVIHLRARKGSVETQSGDEVSRAIPQQPYS

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_1426 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1426 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000003405	1 retrocopy	retro_itri_1426 ,