RetrogeneDB ID: retro_itri_1853

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394129.1:21852..23106(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3BP2
• Ensembl ID: ENSSTOG00000012975
• Aliases: None
• Description: GTPase activating protein (SH3 domain) binding protein 2 [Source:HGNC Symbol;Acc:30291]

Sequence

>retro_itri_1853
AGGTTTTATGGTCAGCATTCTTCCTATGTTCATGGTGGAGTAGATGCTAGTGGAAAGCCCCAGGAAGCTGTTTATGACCA
AAATGATATACACCACAAAGTGTTATCTCTGAACTTCAGTGAGTGTCATACTAAGATTCGTCATGTGGATGCCCATGCAA
CCTTGAGTGATGGAGTAGTTGTTCTGGTCATGGGTTTACTGTCAAACAGTGGACAGCCAGAAAGGAAGTTTATGCAGACC
TTTGTTCTGGCTCCTGAAGGATCTGTTCCAAATAAATTTTATGTTCACAATGATATGTTTCACTATGAAGATGAAGTACT
TGGTGATTCGGAACCAGAACTTGATGAAGAGTCAGAAGATGAAGTAGAAGAGGGACAAGAAGAAAGACAACCATCTCCTG
AACCTGTGCAAGAAAATGCTAACAGTGGTTACTATGAAGCTCACCCTGTGACTAATGGCATAGAGGAACCTTTGGAAGAA
TCCTCTCATGACCCTGAACCCGAGCCAGAATCTGAAACAAAGACTGAAGAGCTGAAACCACAGGTGGAAGAAAAGAACTT
AGAAGAATTAGAGGAGAAGTCTGCTACTCATCCTCCTGCAGAACCAGTTTCTCTGCCACAAGAACCACCAAAGCCAAGAG
TTGAAGCTAAACCAGAATTTCAATCTCAGCCACCATGTATGCATAAACAACGACCTAGGGAATGACCTGGTTTTCCTCCC
AGATGTCCAAGACCCGGCAGAGGAGATATAGAGCAGAATGACTCTGACAACCATAGAATAATTCGCTATCCAGACAGTCA
TCAGCTTTTTGTTGGTAACTTGCCACATGATATTGATGAAAATGAACTAAAAGAGTTCTTTATGCATTTTGGAAACGTTG
TGGAACTTCACATCAATACCAAGGGTGTTGGGGGAAAGCTTCCAAATTTTGGTTTTGTGATTTTTGATGACTCTGAACCA
GTTCAGAGAATCTTAATCGCAAAAACCATTATGTTTCGAGTGGAGGTATGTTTAAATGTGGAAGAGAAGAAAACCAGACC
TGCAAGAGAGCAAGAAACCAGAGGTGGTGGTGATGATCACAGAGATATTAGGCGCAAAGATTGAGGTCCTGGTGGTCCAC
GTGGTATTGTAGGTGGTGGAATGATGCGGGACCGTGATGGAAGAGGACCTCCTCCAAGAGGCGGCCTGGCGCAGAAACTT
GGCTCTGGGAGAGGAACTGGGCAAATGGAAGGCTATTTCACACGACAGCGTCGC

Alignment

ORF - retro_itri_1853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.34 %
• Parental protein coverage: 93.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFYGRNSSYVHGGVDASGKPQEAVYGQNDIHHKVLSLNFSECHTKIRHVDAHATLSDGVVVQVMGLLSNS
          RFYG..SSYVHGGVDASGKPQEAVY.QNDIHHKVLSLNFSECHTKIRHVDAHATLSDGVVV.VMGLLSNS
Retrocopy RFYGQHSSYVHGGVDASGKPQEAVYDQNDIHHKVLSLNFSECHTKIRHVDAHATLSDGVVVLVMGLLSNS

Parental  GQPERKFMQTFVLAPEGSVPNKFYVHNDMFRYEDEVFGDSEPELDEESEDEVEEEQEERQPSPEPVQENA
          GQPERKFMQTFVLAPEGSVPNKFYVHNDMF.YEDEV.GDSEPELDEESEDEVEE.QEERQPSPEPVQENA
Retrocopy GQPERKFMQTFVLAPEGSVPNKFYVHNDMFHYEDEVLGDSEPELDEESEDEVEEGQEERQPSPEPVQENA

Parental  NSGYYEAHPVTNGIEEPLEESSHDPEPEPESETKTEELKPQVEEKNLEELEEKSTTPPPAEPVSLPQEPP
          NSGYYEAHPVTNGIEEPLEESSHDPEPEPESETKTEELKPQVEEKNLEELEEKS.T.PPAEPVSLPQEPP
Retrocopy NSGYYEAHPVTNGIEEPLEESSHDPEPEPESETKTEELKPQVEEKNLEELEEKSATHPPAEPVSLPQEPP

Parental  KPRVEAKPEVQSQPPRVREQRPRERPGFPPRGPRPGRGDMEQNDSDNRRIIRYPDSHQLFVGNLPHDIDE
          KPRVEAKPE.QSQPP....QRPRE.PGFPPR.PRPGRGD.EQNDSDN.RIIRYPDSHQLFVGNLPHDIDE
Retrocopy KPRVEAKPEFQSQPPCMHKQRPRE*PGFPPRCPRPGRGDIEQNDSDNHRIIRYPDSHQLFVGNLPHDIDE

Parental  NELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRILIAKPIMFRGEVRLNVEEKKTRAARE
          NELKEFFM.FGNVVEL.INTKGVGGKLPNFGFV.FDDSEPVQRILIAK.IMFR.EV.LNVEEKKTR.ARE
Retrocopy NELKEFFMHFGNVVELHINTKGVGGKLPNFGFVIFDDSEPVQRILIAKTIMFRVEVCLNVEEKKTRPARE

Parental  RETRGGGDDRRDIRRNDRGPGGPRGIVGGGMMRDRDGRGPPPRGGMAQKLGSGRGTGQMEGRFTGQRR
          .ETRGGGDD.RDIRR.D.GPGGPRGIVGGGMMRDRDGRGPPPRGG.AQKLGSGRGTGQMEG.FT.QRR
Retrocopy QETRGGGDDHRDIRRKD*GPGGPRGIVGGGMMRDRDGRGPPPRGGLAQKLGSGRGTGQMEGYFTRQRR

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_1853 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1853 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019897	1 retrocopy	retro_cjac_4164,
Echinops telfairi	ENSETEG00000016219	1 retrocopy	retro_etel_86,
Gorilla gorilla	ENSGGOG00000014947	1 retrocopy	retro_ggor_1763,
Otolemur garnettii	ENSOGAG00000000157	1 retrocopy	retro_ogar_810,
Ictidomys tridecemlineatus	ENSSTOG00000012975	1 retrocopy	retro_itri_1853 ,