RetrogeneDB ID: retro_itri_1709

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393647.1:977952..979388(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000000129
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000026227
• Aliases: None
• Description: None

Sequence

>retro_itri_1709
GGTGGCTGTACTCTGGGCATGGCCCCTCGCCACAGCGCCTGCCGCCACTTCTCCTGTGTGAGTTTACACAGGAACAAGCC
CCGGCCGGGCGTGAGAAACTCCGCCAGCGTTTGAATGAGGAGAAGCTGGAGATGCTGCGATGGAAGCTTTCGGCCTCTGG
AGTACCTGAGGGGGAGGCAGGCCTGCCACTTACAGTGGATGCCATCAATGATGCCTCTGTGGAAGAAGACTTGGCAGTGG
CTGTGGCAGGCGGCCGGTTGGAAGAAGTGAACTTCCTGCAACCCCACCCAGCTCTGCGGCGGCGTGCTCTGCTGCAGGCT
TCGGGTGTGCGAAGGATCGACCGTGAGGAGAAGCGGGAACTGAAGGCGCTGCGCCAATCCCGTGAGGACTGTGGCTGTCG
CTGTGATAGGGTCTGTGACCCTGAGACCTGCAGCCGCAGCTTGGCGGGTATCAAATGCCAGAGGGACCACACAGGGTTCC
CCTGTGGCTGCTGTAAGGAGGGCTGTGAGAACCCCAATGGCCGTGTGGAATTTAATCAGGCACGTGTGCAGACCCATTTC
ATCCACACGCTCATGCGCCTGCAGCTGGAGCAGGGGGCTGAGAGCCTTGGAGAGCTGAAGGCCCCTGCACAGGGCAGCCC
AGCCAACCCTGGCGAGCAGGACATGGTGTCCTCTTTCCCGCTGGCCAGCCCCCCAGCAAGCAGTGAGCTTGGAGACAATA
GCTGCAGCAGTGACATGACCGATTCTTCCACGACATCTTCCTCATCAGGCGCTAGTGAGGCCCCAGACCACCCCACCCAT
CCAGGCCTGCCTGGTCCTGGCTTCCAGCCAAGCATGGATGATGACAGCCTGGCACGGATCCTGAGTTTCAGTGACTCTGA
CCTTGGTGGGGAGGAGGAGGAAGAGGAAGGGGGTGTGGGGAACCTGGACAACCTCAGCTGCTTTTACCCAACTGACATCT
TTACTGGTGACCCTGGTGGCCTGGCCAGCTGGACCCACAACTATTCTGGCACTAGCTTTGTGCCTGGTATCCTGGATGAG
AATGCCAACCTGGATGCTAGCTGCTTCCTAAATGGCTTTGAAGGGTTGAGAGAAAGTAGCCTCCCTGGCACCTCGGTGCC
ACTCAGTGTGGACATTCACCAGAGCAACTCAGTGGACCTCAGCATGTCTTCCTGCGACTCCTTCGAGCTACTCCAGTCTC
TGCCAGATTACAGTTTGGGGCCTCACTATACCTCCCAGAAGGTGCCTGGCAGCCTGGACAACCTCGAGGCATCCCACGGC
CCCTTGCCTTGCCTCTCTCCACCGGGGGATGGCAGCACTTGCTTCCTGGAGTCCCTCATGGGCTTGTCTGAACCAGTTGC
TGACTCCGTGGCCCCCTTCATCAACAGCCAGTTTGAGGACACTGCCCCGGCCTCTCTGGTAGAGCCTGTGCAGGTC

Alignment

ORF - retro_itri_1709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.83 %
• Parental protein coverage: 91.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGCTLGMAPRHSTCRHFS-LCEFTQEQARARREKLRQRLKEEKLEMLRWKLSASGVPEGEAGLPLTVDAI
          GGCTLGMAPRHS.CRHFS.LCEFTQEQA.A.REKLRQRL.EEKLEMLRWKLSASGVPEGEAGLPLTVDAI
Retrocopy GGCTLGMAPRHSACRHFS<LCEFTQEQAPAGREKLRQRLNEEKLEMLRWKLSASGVPEGEAGLPLTVDAI

Parental  NDASVEEDLAVAVAGGRLEEVNFLQPHPARRRRALLRASGVRRIDREEKRELKALRQSREDCGCRCDRVC
          NDASVEEDLAVAVAGGRLEEVNFLQPHPA.RRRALL.ASGVRRIDREEKRELKALRQSREDCGCRCDRVC
Retrocopy NDASVEEDLAVAVAGGRLEEVNFLQPHPALRRRALLQASGVRRIDREEKRELKALRQSREDCGCRCDRVC

Parental  DPETCSCSLAGIKCQMDHTGFPCGCCKEGCENPNGRVEFNQARVQTHFIHTLTRLQLEQGAERLGELEAP
          DPETCS.SLAGIKCQ.DHTGFPCGCCKEGCENPNGRVEFNQARVQTHFIHTL.RLQLEQGAE.LGEL.AP
Retrocopy DPETCSRSLAGIKCQRDHTGFPCGCCKEGCENPNGRVEFNQARVQTHFIHTLMRLQLEQGAESLGELKAP

Parental  AQGSPANPGEQDMVSSFPLASPPASSELGDNSCSSDMTDSSTTSSSSGASEAPDHPTHPGLPGPGFQPSM
          AQGSPANPGEQDMVSSFPLASPPASSELGDNSCSSDMTDSSTTSSSSGASEAPDHPTHPGLPGPGFQPSM
Retrocopy AQGSPANPGEQDMVSSFPLASPPASSELGDNSCSSDMTDSSTTSSSSGASEAPDHPTHPGLPGPGFQPSM

Parental  DDDSLARILSFSDSDLGGEEEEEEGGVGNLDNLSCFYPTDIFTGDPGGLVSWTHNYSGTSFVPGILDENA
          DDDSLARILSFSDSDLGGEEEEEEGGVGNLDNLSCFYPTDIFTGDPGGL.SWTHNYSGTSFVPGILDENA
Retrocopy DDDSLARILSFSDSDLGGEEEEEEGGVGNLDNLSCFYPTDIFTGDPGGLASWTHNYSGTSFVPGILDENA

Parental  NLDASCFLNGFEGLRESSLPGTSVPPSVDIHQSNSVDLSLSSCDSFELLQSLPDYSLGPHYTSQKAPGSL
          NLDASCFLNGFEGLRESSLPGTSVP.SVDIHQSNSVDLS.SSCDSFELLQSLPDYSLGPHYTSQK.PGSL
Retrocopy NLDASCFLNGFEGLRESSLPGTSVPLSVDIHQSNSVDLSMSSCDSFELLQSLPDYSLGPHYTSQKVPGSL

Parental  DNLEASHGPLPGLSPPGDGSTCFLESLMGLSEPVADALAPFIDSQFEDTAPASLVEPVQV
          DNLEASHGPLP.LSPPGDGSTCFLESLMGLSEPVAD..APFI.SQFEDTAPASLVEPVQV
Retrocopy DNLEASHGPLPCLSPPGDGSTCFLESLMGLSEPVADSVAPFINSQFEDTAPASLVEPVQV

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_1709 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1709 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	ENSSTOG00000026227	1 retrocopy	retro_itri_1709 ,