RetrogeneDB ID: retro_itri_1678

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393629.1:1188111..1189065(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPBP1
• Ensembl ID: ENSSTOG00000003057
• Aliases: None
• Description: GC-rich promoter binding protein 1 [Source:HGNC Symbol;Acc:29520]

Sequence

>retro_itri_1678
GCTCCTCTCTTAGAATATCCTCCGAATCCTAAATCTAGAGCTCCAAGGATGCTGGTTATTAAGAAAGGTAATACAAAAGA
CTTACAGCTATCTGGATTCCCTGTAGTAGGAAATCTTCAGTCACAGCCAGTTAATAATGGAACTGGTCCGAGTGTTTATA
AAGGCTTAGTCCCTAAACCTGCTGCTCCACCTACAAAACCTACACAGTGGAAAAGCCAAACTAAAGAAAATAAGGTTGGG
ACTTCTTTCCCTCATGAATCTTCATATGGTGATGGCAACTTTAATGCTTTTAAATCAACTGCCAAGAATTTTAGTCCATC
ACTAAATTCAGTGAAAGAGTGTAATCGTTCAAATTCCTCTTCACCTGTTGACAAACTTAATCAGCAGCCTCGTCTAACCA
AACTGACACGAATGCGCACTGATAAGAAGAGTGAATTTTTGAAAGCATTGAAAAGGGACAGAGTAGAAGAAGAACATGAA
GATGAAAGCCATGTTGGCTCAGAGAAGGATGAAGACTCATTTAATTTGCATAACAGCAATAGTACTCACTAAGAAAGGGA
TATAAACAGAAACTTTGATGAAAATGAAATTCCACAAGAGAATGGCAATGCCTCAGTGATTTCCCAACAGATCATTCGGT
CTTCAACCTTTCTGCAAACTGATGTTCTTTCCAGTTCACTTGAGGCAGAACACAGATTGTTAAAGGAAATGGGCTGGCAG
GAAGACAGTGAAAATGATGAAACATGTGCTCCCTTAACTGAGGATGAAATGAGAGAATTCCAAGTTATTAGTGAACAGTT
GCAGAAGAATGGTCTGAGAAAAAATGGTATTTTGAAAAATGGCCTGATCTGTGACTTCAAGTTTGGACCCTGGAAAAACA
GCACTTTCAAACCCACAATTGAGAATGATGACACAGAGACAAGTAGCTGTGACACATCAGATGATGATGATGTA

Alignment

ORF - retro_itri_1678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.86 %
• Parental protein coverage: 67.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGVWEYPPNPKSRAPRMLVIKKGNTKDLQLSGFPVVGNLQSQPVKNGTGPSVYKGLVPKPAAPPTKPTQW
          A...EYPPNPKSRAPRMLVIKKGNTKDLQLSGFPVVGNLQSQPV.NGTGPSVYKGLVPKPAAPPTKPTQW
Retrocopy APLLEYPPNPKSRAPRMLVIKKGNTKDLQLSGFPVVGNLQSQPVNNGTGPSVYKGLVPKPAAPPTKPTQW

Parental  KSQTKENKVGTSFPHESSYGVGNFNAFKSTAKNFSPSPNSVKECNRSNSSSPVDKLNQQPRLTKLTRMRT
          KSQTKENKVGTSFPHESSYG.GNFNAFKSTAKNFSPS.NSVKECNRSNSSSPVDKLNQQPRLTKLTRMRT
Retrocopy KSQTKENKVGTSFPHESSYGDGNFNAFKSTAKNFSPSLNSVKECNRSNSSSPVDKLNQQPRLTKLTRMRT

Parental  DKKSEFLKALKRDRVEEEHEDESHAGSEKDEDSFNLHNSNSTHQERDINRNFDENEIPQENGNASVISQQ
          DKKSEFLKALKRDRVEEEHEDESH.GSEKDEDSFNLHNSNSTH.ERDINRNFDENEIPQENGNASVISQQ
Retrocopy DKKSEFLKALKRDRVEEEHEDESHVGSEKDEDSFNLHNSNSTH*ERDINRNFDENEIPQENGNASVISQQ

Parental  IIRSSTFPQTDVLSSSLEAEHRLLKEMGWQEDSENDETCAPLTEDEMREFQVISEQLQKNGLRKNGILKN
          IIRSSTF.QTDVLSSSLEAEHRLLKEMGWQEDSENDETCAPLTEDEMREFQVISEQLQKNGLRKNGILKN
Retrocopy IIRSSTFLQTDVLSSSLEAEHRLLKEMGWQEDSENDETCAPLTEDEMREFQVISEQLQKNGLRKNGILKN

Parental  GLICDFKFGPWKNSTFKPTIENDDTETSSSDTSDDDDV
          GLICDFKFGPWKNSTFKPTIENDDTETSS.DTSDDDDV
Retrocopy GLICDFKFGPWKNSTFKPTIENDDTETSSCDTSDDDDV

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_1678 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1678 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015104	1 retrocopy	retro_cjac_3961,
Microcebus murinus	ENSMICG00000014678	1 retrocopy	retro_mmur_1198,
Myotis lucifugus	ENSMLUG00000007462	1 retrocopy	retro_mluc_155,
Monodelphis domestica	ENSMODG00000019540	1 retrocopy	retro_mdom_283,
Otolemur garnettii	ENSOGAG00000013991	1 retrocopy	retro_ogar_1077,
Ictidomys tridecemlineatus	ENSSTOG00000003057	1 retrocopy	retro_itri_1678 ,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243,