RetrogeneDB ID: retro_itri_371

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393286.1:17901987..17902524(-)
• Located in intron of: ENSSTOG00000015649

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD276
• Ensembl ID: ENSSTOG00000021193
• Aliases: None
• Description: CD276 molecule [Source:HGNC Symbol;Acc:19137]

Sequence

>retro_itri_371
ATGCTGCACAGACTGGTCAGCCCTGGCATGGTGCACGTGTGGGCACAGCCCTGGAGGTACTGTGCTTTTGCCTCACAGGA
GCTGTGGAGGTCCAGAACCCTGAAGACCCGGTGGTAGCCCTGGGTGGGCACTGATGCCACCCTGCACTGCTCCTTCTCAC
CTGAGCCTGGCTTCAGCCTGGTACAGCTCAACCTCATCTGGCAGCTGACGGACACCAAACAGCTGGTGCATAGCTTTGCT
GAGGGCCGGGACCAGGGCAGAGCCTATGCCAACCGCACCATGCTCTTCCCAGACCTGCTGGCACAGGGCAACACATTCCT
GAGGCTGCAAGGTGTACATGTGGCTGATGAAAGCAGCTTCACTTGCTTCTTAAGCATTCGGGACTTTGGCAGTGCTGCTA
TCAGCCTGCAGGTGGCAGCCCCCTATTCAAAACCCAGCGTGACCATGGAGCCCAGCAAGGACCTGGGGACAGTCACCAGG
GCTACCCTGAGGCTGAGGTGTTCCACAGGATGGGCAGGGTGCATCCTTGACTGGCAA

Alignment

ORF - retro_itri_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.56 %
• Parental protein coverage: 56.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLHRLVSPGM-GVHVGTALGVLCFCLTGAVEVQVPEDPVVAL-VGTDATLHCSFSPEPGFSLAQLNLIWQ
          MLHRLVSPGM.G..VGTAL.VLCFCLTGAVEVQ.PEDPVVAL.VGTDATLHCSFSPEPGFSL.QLNLIWQ
Retrocopy MLHRLVSPGM<GARVGTALEVLCFCLTGAVEVQNPEDPVVAL>VGTDATLHCSFSPEPGFSLVQLNLIWQ

Parental  LTDTKQLVHSFAEGRDYGSAYANRTMLFPDLLAQGNASLRLQGVRVADEGSFTCFVSIRDFGSAAVSLQV
          LTDTKQLVHSFAEGRD.G.AYANRTMLFPDLLAQGN..LRLQGV.VADE.SFTCF.SIRDFGSAA.SLQV
Retrocopy LTDTKQLVHSFAEGRDQGRAYANRTMLFPDLLAQGNTFLRLQGVHVADESSFTCFLSIRDFGSAAISLQV

Parental  AAPYSKPSMTLEPSKDLRPGDMVTITCFSHRGYPEAEVIWQ
          AAPYSKPS.T.EPSKDL......T.......G.......WQ
Retrocopy AAPYSKPSVTMEPSKDLGTVTRATLRLRCSTGWAGCILDWQ

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_371 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_371 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000000639	1 retrocopy	retro_lcha_122,
Ictidomys tridecemlineatus	ENSSTOG00000021193	1 retrocopy	retro_itri_371 ,