RetrogeneDB ID: retro_itri_1535

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393533.1:599910..600726(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAB1
• Ensembl ID: ENSSTOG00000008615
• Aliases: None
• Description: protein kinase, AMP-activated, beta 1 non-catalytic subunit [Source:HGNC Symbol;Acc:9378]

Sequence

>retro_itri_1535
ATGGGAAACACCACCAGCGACCGGGTGTCCGGGGAGCGCCACGGCGCCAAGGCTGCTCGCGCGGAAGGCGGCGGCGGCCA
TGCCCCCGGCAAGGAGCACAAGATCATGGTCGGGAGCACCGACGACCCCAGCGTTTTCAGCCTGCCGGACTCCAAGCTCC
CTGGGGACAAAGAGTTTGTATCATGGCAGCAAGATTTGGACGACTCTGAAAAGCCTACGCAGCAGGCCCGGCCTACTGTT
ATCCGTTGGTCTGAAGGAGGCAAGGAGGTCTTCATTTCTGGGTCCTTCAACAACTGGAGCACCAAGATTCCACTGATCAA
GAGCCATAATGACTTCGTTGCCATCCTGGACCTCCCCGAGGGAGAGCACCAATACAAGTTTTTTGTAGATGGACAGTGGG
TTCATGATCCATCAGAGCCTGTGGTTACCAGTCAGCTTGGCATGATTAACAATTTGATCCATGTCAAGAAATCTGATTTT
GAGGTGTTTGATGCTTTAAAACTAGATTCTATGGAAAGTTCTGAGACATCTTGTCAAGACCTTTCCAGTTCACCCCCGGG
GCCTTATGGTCAAGAAATGTATGTATTTTGATCTGAAGAGAGATTCAAATCCCCACCCATCCTTCCTCCTCACCCACTCC
AAGTTATTCTTAACAAGGACACTAATATTTCTTGTGACCCAGCCCTACTTCCTGAGTCCAACCATGTTATGCTGAGCCAT
CTCTATGCATTATCTATTAAGGACAGTGTGATGGTTCTTAGTGCAACCCATCGTTACAAGAAGAAGTATGTCACTACACT
GCTGTACAAGCCCATC

Alignment

ORF - retro_itri_1535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNTSSERAALERQGGHKTPRRDSSGGTKDGDRPKILMDSPEDADLFHSEEIKAPEKEEFLAWQHDLEVN
          MGNT.S.R...ER.G..K..R....GG...G...KI...S..D...F.....K.P...EF..WQ.DL...
Retrocopy MGNTTSDRVSGERHGA-KAARAEGGGGHAPGKEHKIMVGSTDDPSVFSLPDSKLPGDKEFVSWQQDLDDS

Parental  DKAPAQARPTVFRWTGGGKEVYLSGSFNNWS-KLPLTRSHNNFVAILDLPEGEHQYKFFVDGQWTHDPSE
          .K...QARPTV.RW..GGKEV..SGSFNNWS.K.PL..SHN.FVAILDLPEGEHQYKFFVDGQW.HDPSE
Retrocopy EKPTQQARPTVIRWSEGGKEVFISGSFNNWSTKIPLIKSHNDFVAILDLPEGEHQYKFFVDGQWVHDPSE

Parental  PIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQKCSDVS--ELSSSPPGPYHQEPYVSKPEERFKAPPILP
          P.VTSQLG..NN.I.VKK.DFEVFDAL..DS...S..S...LSSSPPGPY.QE.YV...EERFK.PPILP
Retrocopy PVVTSQLGMINNLIHVKKSDFEVFDALKLDSMESSETSCQDLSSSPPGPYGQEMYVF*SEERFKSPPILP

Parental  PHLLQVILNKDTGISCDPALLPEPNHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI
          PH.LQVILNKDT.ISCDPALLPE.NHVML.HLYALSIKD.VMVLSATHRYKKKYVTTLLYKPI
Retrocopy PHPLQVILNKDTNISCDPALLPESNHVMLSHLYALSIKDSVMVLSATHRYKKKYVTTLLYKPI

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_1535 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1535 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000006584	1 retrocopy	retro_meug_2055,
Monodelphis domestica	ENSMODG00000015269	1 retrocopy	retro_mdom_1984,
Ictidomys tridecemlineatus	ENSSTOG00000008615	1 retrocopy	retro_itri_1535 ,