RetrogeneDB ID: retro_itri_1718

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393657.1:690863..691990(+)
• Located in intron of: ENSSTOG00000010518

Retrocopy information

• Ensembl ID: ENSSTOG00000019662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPN1
• Ensembl ID: ENSSTOG00000006379
• Aliases: None
• Description: GPN-loop GTPase 1 [Source:HGNC Symbol;Acc:17030]

Sequence

>retro_itri_1718
TCAAAGGGAAAGATGGCAGCCCCGGTGGCAGCCGCAGATTCTGGGGCTTCGGGACCTCCTAATCTCCCAGTGTGTCTGTT
GGGAATGGCAGGTTCCAGAAAAAACACTTTTTTACAGAGGCTAAAGAGGCACCTGCATAGGCAAAGCTGTCCTCTTTACG
TGATCAACTTGGACCTAGCTATGCACGAAGTCCCCTTTCCTGCCAATATTGATATTTGTGACACTATGAAGTATAAAGAA
GTCATGAAACAATATGACTTGGGCCCAATGGTGGCATAGTAACCTCTCTCAATCTCTTTGCTACCAGATTTGATCAGGTG
ATGAAATTTATTGAGAAGGCCCAGAACACATCTAAATATGTCTTGATTGACACACCTGGGCAGATTGAGGTATTCAATCT
GCTCAGCTTCTGGAACAATCATCACTGAGGCCCTGGCATCCTCACTCCCAACAGTTGTCATCTATGTAATGGACACATCA
AGAAGTACTAACCCAGTGACGTTTATGTCGAATATGCTGTATGCCTGCAGCATCTTGTACAAAACCAAGCTGCCTTTCAT
TATGGTTATGAACAAGACTGACATCATTGATCACAGCTTTGCAGTGGAATGGATGCAGGATTTTGAGGCTTTCCAAGATG
CCTTGAATCAAGCAACTACATATGTGAGTAACCTGACCCGTTCAATGAGCCTGGTATCAGATGAGTTTTACAGCTCACTC
AGGGTGGTGGGTGTCTCTGCTGTTGTGGGCACTGGCTTCGATGAACTCTTTGTGCAAATCACCAGGGCTGCAGAAGAATA
TGAAAGGGAGTATCGTCCTGAAGATGAACGTCTGAAGAAATCGTTGGCCAGTGCACAGAGTGAACAGCAGAAAGAACAAC
TGGACCGCCTTCGGAAAGATATGGGCTCTGTAGCCTTAGACACAGGGACTGCCAAAGAGAGCGGATCTCCTGTGTTGGAC
CCTCTGACTTAACCCTGACTCAAGGAACCTTGGATGAAGAGGATGAGGAAGCTGACAGTGATACTGACGACACTGACCAC
AGAGTTACAGAGGAAAGTCACCAAGAGCCAGCATTTCAGAATTTTATGCAAGAATCCATGGCACAGTACTGGAAGAGAAA
CAACAAA

Alignment

ORF - retro_itri_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.6 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ARGKMAAPVAAADSGTSGTPNLPVCLLVLGMAGSGKTTFVQRLTGHLHRQSCPPYVINLDPAVHEVPFPA
          ..GKMAAPVAAADSG.SG.PNLPVCLL..GMAGS.K.TF.QRL..HLHRQSCP.YVINLD.A.HEVPFPA
Retrocopy SKGKMAAPVAAADSGASGPPNLPVCLL--GMAGSRKNTFLQRLKRHLHRQSCPLYVINLDLAMHEVPFPA

Parental  NIDIRDTVKYKEVMKQYGLGP-NGGIVTSLNLFATRFDQVMKFIEKAQNTSKYVLIDTPGQIEVFTW-SA
          NIDI.DT.KYKEVMKQY.LGP.NGGIVTSLNLFATRFDQVMKFIEKAQNTSKYVLIDTPGQIEVF...SA
Retrocopy NIDICDTMKYKEVMKQYDLGP<NGGIVTSLNLFATRFDQVMKFIEKAQNTSKYVLIDTPGQIEVFNL>SA

Parental  SGTIITEALASSFPTVVIYVMDTSRSTNPVTFMSNMLYACSILYKTKLPFIVVMNKTDIIDHSFAVEWMQ
          SGTIITEALASS.PTVVIYVMDTSRSTNPVTFMSNMLYACSILYKTKLPFI.VMNKTDIIDHSFAVEWMQ
Retrocopy SGTIITEALASSLPTVVIYVMDTSRSTNPVTFMSNMLYACSILYKTKLPFIMVMNKTDIIDHSFAVEWMQ

Parental  DFEAFQDALNQETTYVSNLTRSMSLVLDEFYSSLRVVGVSAVVGTGFDELFVQITSAAEEYEREYRPEYE
          DFEAFQDALNQ.TTYVSNLTRSMSLV.DEFYSSLRVVGVSAVVGTGFDELFVQIT.AAEEYEREYRPE.E
Retrocopy DFEAFQDALNQATTYVSNLTRSMSLVSDEFYSSLRVVGVSAVVGTGFDELFVQITRAAEEYEREYRPEDE

Parental  RLKKSLASAQSEQQKEQLDRLRKDMGSVALDTGTAKESGSPVLDP-SDLILTRGTLDEEDEEADSDTDDI
          RLKKSLASAQSEQQKEQLDRLRKDMGSVALDTGTAKESGSPVLDP.SDL.LT.GTLDEEDEEADSDTDD.
Retrocopy RLKKSLASAQSEQQKEQLDRLRKDMGSVALDTGTAKESGSPVLDP<SDLTLTQGTLDEEDEEADSDTDDT

Parental  DHRVTEESHEEPAFQNFMQESMAQYWKRNNK
          DHRVTEESH.EPAFQNFMQESMAQYWKRNNK
Retrocopy DHRVTEESHQEPAFQNFMQESMAQYWKRNNK

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_1718 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1718 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013421	1 retrocopy	retro_eeur_146,
Microcebus murinus	ENSMICG00000014941	1 retrocopy	retro_mmur_649,
Ictidomys tridecemlineatus	ENSSTOG00000006379	2 retrocopies	retro_itri_1428, retro_itri_1718 ,
Tupaia belangeri	ENSTBEG00000007425	1 retrocopy	retro_tbel_3907,