RetrogeneDB ID: retro_itri_356

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393286.1:7957848..7959879(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019916
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRKCH
• Ensembl ID: ENSSTOG00000009567
• Aliases: None
• Description: protein kinase C, eta [Source:HGNC Symbol;Acc:9403]

Sequence

>retro_itri_356
AAGTTCAATGGCTATTTGAGGGTCCGCATTGGCGAGGCGGTGGGGCTGCAGCCAACCCGCTGGTCCCTGCGCCACTCGCT
CTTCAAGAAGGGCTACCAGCTGCTGGACCCCTACCTGACAGTGAGCGTGGACCAGGTACGCGTGGGCCAGACCAGCACCA
AGCAGAAGACCAACAAACCCACGTACAACGAGGAGTTCTGCGCTAACGTCACCGACGGCGGCCACCTTGAGCTGGCCGTA
TTCCACGAGACACCCCTGGGTTGCGACCACTTTGTGGCCAACTGCACCCTGCAATTCCAGGAGTTGCTGCGCACGGCTGG
CACCTCGGACACCTTCGAGGGCTGGGTGGATCTGGAGCCTGAGGGGAAAGTATTTGTGGTAATAACCCTCACAGGAAGTT
TCACTGAAGCCACTCTCCAGAGAGACCGAATCTTCAAACATTTTACCAGAAAGCGCCAAAGGGCTATGCGAAGGCGGGTC
CACCAGATCAACGGACACAAGTTTATGGCCACATACCTGAGGCAGCCCACCTACTGCTCTCACTGCAGAGAGTTCATCTG
GGGAGTATTTGGGAAACAGGGTTATCAATGCCAAGTGTGCACCTGTGTCGTCCATAAACGCTGCCATCATCTAATTGTTA
CAGCCTGTACTTGCCAAAACAATATCAACAAAGTGGATTCAAAGATTGCTGAACAGAGGTTTGGAATCAACATCCCACAC
AAATTCAGCATCCACAACTACAAAGTGCCAACGTTTTGCCATCACTGTGGCTCCCTGCTCTGGGGCATGATGCGATAAGG
ACTTCAGTGTAAAATATGTAAAATGAATGTACATATTCGATGTCAAGCAAATGTGGCCCCTAACTGTGGGGTAAATGCGG
TAGAGCTTGCCAAGACCCTGGCAGGGATGGGCCTCCAGCCTGGAAATATCTCTCCAACCTCGAAACTCGTTTCTAGATCG
ACCCTAAGAAGACAGGGAAAGGATGGCACCAAAGAAGGAAATGGGGTTGGGGTTAATTCTTCCAACCGATTTGGTATCGA
CAACTTCGAATTCATCCGAGTGTTGGGGAAGGGGAGTTTTGGGAAGGTGATGCTTGCAAGGATAAAAGAAACAGGAGACC
TCTATACTGTGAAGGTGCTGAAGAAGGAGGTGATCCTCCAGGATGACGATGTGGAATGCACCATGACTGAGAAGAGGATC
CTGTCTTTGGCCCACAATCACCCCTTCCTCACCCAGTTGTTTTGCTGCTTCCAGACCCCTGACCGCCTGTTTTTCGTGAT
GGAGTTTGTGAATGGCGGAGACTTGATGTTCCACATTCAGAAATCCCAGCGTTTTGATGAGGCACGGGCTTGTTTCTATG
CTGCGGAGATCATTTCTGCGCTCATGTTCCTACATGAAAAGGAAATCATCTATCGAGATCTGAAACTAGACAATGTGCTG
TTGGACCATGAGGGTCACTGTAAACTGGCAGACTTCGGAATGTGCAAGGAGGGGATCTGTAATGGCGTCACCACAGCCAC
ATTCTGTGGAACACCTGACTACATTGCTCCAGAGATCCTCCAGGAAATGCTGTATGGGCCTGCTGTGGATTGGTGGGCCA
TGGGTGTGTTGCTCTACGAGATGCTCTGTGGTCATGCACCCTTTGAGGCTGAGAATGAAGACGACCTCTTTGAGGACATC
CTGAATGATGAGGTGGTCTACCCTACCTGGCTCCATGAAGATGCCACAGGGATCCTAAAATCTTTCATGACCAAGAACCC
CACCATGCGCTTGGGCAGCCTGACTCAGGGAGGAGAGCATGCTATCTTGAGACATCCTTTCTTTAAGGAAATTGACTGGG
CCCAACTGAACCATCGCCAACTGGAACCACCCTTCCGACCCAGAATCAAATCCCGAGAGGATGTCAGTAATTTTGACCCT
GACTTCATAAAAGAAGAGCCAATTTTAACTCCCATTGATGAGGGACACCTGCCTATGATTAATCAGGATGAGTTTAGAAA
CTTTTCCTATGTGTCTCCAGAATTGCAACCT

Alignment

ORF - retro_itri_356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.38 %
• Parental protein coverage: 99.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KFNGYLRVRIGEAVGLQPTRWSLRHSLFKKGYQLLDPYLTVSVDQVRVGQTSTKQKTNKPTYNEEFCANV
          KFNGYLRVRIGEAVGLQPTRWSLRHSLFKKGYQLLDPYLTVSVDQVRVGQTSTKQKTNKPTYNEEFCANV
Retrocopy KFNGYLRVRIGEAVGLQPTRWSLRHSLFKKGYQLLDPYLTVSVDQVRVGQTSTKQKTNKPTYNEEFCANV

Parental  TDGGHLELAVFHETPLGYDHFVANCTLQFQELLRTAGTSDTFEGWVDLEPEGKVFVVITLTGSFTEATLQ
          TDGGHLELAVFHETPLG.DHFVANCTLQFQELLRTAGTSDTFEGWVDLEPEGKVFVVITLTGSFTEATLQ
Retrocopy TDGGHLELAVFHETPLGCDHFVANCTLQFQELLRTAGTSDTFEGWVDLEPEGKVFVVITLTGSFTEATLQ

Parental  RDRIFKHFTRKRQRAMRRRVHQINGHKFMATYLRQPTYCSHCREFIWGVFGKQGYQCQVCTCVVHKRCHH
          RDRIFKHFTRKRQRAMRRRVHQINGHKFMATYLRQPTYCSHCREFIWGVFGKQGYQCQVCTCVVHKRCHH
Retrocopy RDRIFKHFTRKRQRAMRRRVHQINGHKFMATYLRQPTYCSHCREFIWGVFGKQGYQCQVCTCVVHKRCHH

Parental  LIVTACTCQNNINKVDSKIAEQRFGINIPHKFSIHNYKVPTFCDHCGSLLWGIMRQGLQCKICKMNVHIR
          LIVTACTCQNNINKVDSKIAEQRFGINIPHKFSIHNYKVPTFC.HCGSLLWG.MR.GLQCKICKMNVHIR
Retrocopy LIVTACTCQNNINKVDSKIAEQRFGINIPHKFSIHNYKVPTFCHHCGSLLWGMMR*GLQCKICKMNVHIR

Parental  CQANVAPNCGVNAVELAKTLAGMGLQPGNISPTSKLVSRSTLRRQGKDGTKEGNGVGVNSSNRFGIDNFE
          CQANVAPNCGVNAVELAKTLAGMGLQPGNISPTSKLVSRSTLRRQGKDGTKEGNGVGVNSSNRFGIDNFE
Retrocopy CQANVAPNCGVNAVELAKTLAGMGLQPGNISPTSKLVSRSTLRRQGKDGTKEGNGVGVNSSNRFGIDNFE

Parental  FIRVLGKGSFGKVMLARIKETGDLYAVKVLKKDVILQDDDVECTMTEKRILSLARNHPFLTQLFCCFQTP
          FIRVLGKGSFGKVMLARIKETGDLY.VKVLKK.VILQDDDVECTMTEKRILSLA.NHPFLTQLFCCFQTP
Retrocopy FIRVLGKGSFGKVMLARIKETGDLYTVKVLKKEVILQDDDVECTMTEKRILSLAHNHPFLTQLFCCFQTP

Parental  DRLFFVMEFVNGGDLMFHIQKSRRFDEARARFYAAEIISALMFLHEKGIIYRDLKLDNVLLDHEGHCKLA
          DRLFFVMEFVNGGDLMFHIQKS.RFDEARA.FYAAEIISALMFLHEK.IIYRDLKLDNVLLDHEGHCKLA
Retrocopy DRLFFVMEFVNGGDLMFHIQKSQRFDEARACFYAAEIISALMFLHEKEIIYRDLKLDNVLLDHEGHCKLA

Parental  DFGMCKEGICNGVTTATFCGTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFEAI
          DFGMCKEGICNGVTTATFCGTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFE.I
Retrocopy DFGMCKEGICNGVTTATFCGTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFEDI

Parental  LNDEVVYPTWLHEDATGILKSFMTKNPTMRLGSLTQGGEHAILRHPFFKEIDWAQLNHRQLEPPFRPRIK
          LNDEVVYPTWLHEDATGILKSFMTKNPTMRLGSLTQGGEHAILRHPFFKEIDWAQLNHRQLEPPFRPRIK
Retrocopy LNDEVVYPTWLHEDATGILKSFMTKNPTMRLGSLTQGGEHAILRHPFFKEIDWAQLNHRQLEPPFRPRIK

Parental  SREDVSNFDPDFIKEEPILTPIDEGHLPMINQDEFRNFSYVSPELQP
          SREDVSNFDPDFIKEEPILTPIDEGHLPMINQDEFRNFSYVSPELQP
Retrocopy SREDVSNFDPDFIKEEPILTPIDEGHLPMINQDEFRNFSYVSPELQP

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_356 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_356 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	ENSSTOG00000009567	1 retrocopy	retro_itri_356 ,