RetrogeneDB ID: retro_itri_104

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393344.1:2622460..2623615(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000014334
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PRKAR1A
• Ensembl ID: ENSSTOG00000012903
• Aliases: None
• Description: protein kinase, cAMP-dependent, regulatory, type I, alpha [Source:HGNC Symbol;Acc:9388]

Sequence

>retro_itri_104
ATGGCGTCGGGCAGCACCGCGGCCAGTGAGGAGGAGCGCAGCCTCCGCGAGTGCGAGCTGTACGCGCAGAAGCACAACAT
CCAGGCCCTGCTCAAGGACTCCATCGTGCAGCTGTGCACGGCGCGGCCCGAGCGGCCCGTGACGTTCCTCCGGGAATACT
TTGAGAAGTTGGAGAAGGAGGAGGCCAGGCTCTCCCAGAGTCAGCCGACGCCGGGCCCCTGCCCGGAGGAGACGGCGCCG
GCCCAGGCCCAGCCGGCGCCGGCCCAGGCCCAGCCCGTGGTGAAGGGCCGGCGGCGCCGGGGCGCCATCAGCGCCGAAGT
GTGCACGGAGGAAGACGCCGTGTCTTTCGTGCGAAAGGTCATACCCAAGGATTTTAAGACGATCGCCGCCTTAGCCAAAG
CCATTGAGAAGAACGTGCTGTTTTCGCACCTGGATGAAAATGAGAAGAATGACATCTTCTACGCCATGTTCCCCGTCTCC
TTCACGGCGGGAGAGACGGTTATCGAGCAGGGCGACGACGGGGACGTCTTCTACGTGATCGACCAGGGAGAGATGGACGT
GTACGTCAACGACGAATGGACCACCGCCCTCGGGGAAGGAGGGAGCTTTGGAGAACTCGCCCTCATTTACGGGACCCCGC
GAGCAGCCACGGTCAAGGCAAAGACGAGCGTGAAACTGTGGGGGATTGACCGGAGCAGCTACCGAAGGATCCTGATGGGG
AGCACGCTGAAAAAGCGCAAGATGTACGAAGAGTTCCTCAGCAAAGTGTCGATTTTAGAGTCCTTGGACAAGTGGGAGCG
GCTCACGGTAGCGGACGCCCTGGAACCGGTCCAGTTCGAGGACAGGCAGAACATCATGGTGCAGGGGGAACCGGGAGACG
AGTTCTTCATTATTCTGGAGGGGTCGGCTGCCGTGCTGCAGCGTCGGTCCGAAAACGAAGATTTTGTTGAAGTGGGAAGA
TTGGGGCCTTCCGATTATTTTGGAGAAATTGCCCTGCTCAAGAACCGCCCTCGCGCGGCCACGGTGGTTGCACGTGGCCC
CTTGAAGTGTGTGAAGCTGGATCGACTTCGATTTGAACGTGTCCTTGGCCCGTGCTCAGATATCCTCAAACGAAACATCC
AGCAGTACAACATTTTCATGGCACTGTCTGTCTGA

Alignment

ORF - retro_itri_104 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.9 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGSTTASEEERSLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFEKLEKEEAKQIQNLQK
          MASGST.ASEEERSLRECELY.QKHNIQALLKDSIVQLCTARPERP..FLREYFEKLEKEEA...Q....
Retrocopy MASGSTAASEEERSLRECELYAQKHNIQALLKDSIVQLCTARPERPVTFLREYFEKLEKEEARLSQSQPT

Parental  AGT---RTDSREEEISPPPPNPVVKGRRRRGAISAEVYTEEDAASYVRKVIPKDYKTMAALAKAIEKNVL
          .G.....T........P....PVVKGRRRRGAISAEV.TEEDA.S.VRKVIPKD.KT.AALAKAIEKNVL
Retrocopy PGPCPEETAPAQAQPAPAQAQPVVKGRRRRGAISAEVCTEEDAVSFVRKVIPKDFKTIAALAKAIEKNVL

Parental  FSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVYVNNEWATSVGEGGSFGELALIY
          FSHLD.NE..DIF.AMFPVSF.AGETVI.QGD.GD.FYVIDQGEMDVYVN.EW.T..GEGGSFGELALIY
Retrocopy FSHLDENEKNDIFYAMFPVSFTAGETVIEQGDDGDVFYVIDQGEMDVYVNDEWTTALGEGGSFGELALIY

Parental  GTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFE
          GTPRAATVKAKT.VKLWGIDR.SYRRILMGSTL.KRKMYEEFLSKVSILESLDKWERLTVADALEPVQFE
Retrocopy GTPRAATVKAKTSVKLWGIDRSSYRRILMGSTLKKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFE

Parental  DGQKIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKC
          D.Q.I.VQGEPGDEFFIILEGSAAVLQRRSENE.FVEVGRLGPSDYFGEIALL.NRPRAATVVARGPLKC
Retrocopy DRQNIMVQGEPGDEFFIILEGSAAVLQRRSENEDFVEVGRLGPSDYFGEIALLKNRPRAATVVARGPLKC

Parental  VKLDRPRFERVLGPCSDILKRNIQQYNSFVSLSV
          VKLDR.RFERVLGPCSDILKRNIQQYN.F..LSV
Retrocopy VKLDRLRFERVLGPCSDILKRNIQQYNIFMALSV

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_104 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_104 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008621	1 retrocopy	retro_btau_1666,
Homo sapiens	ENSG00000108946	1 retrocopy	retro_hsap_186,
Gorilla gorilla	ENSGGOG00000016507	1 retrocopy	retro_ggor_267,
Macaca mulatta	ENSMMUG00000002194	2 retrocopies	retro_mmul_2498, retro_mmul_393,
Nomascus leucogenys	ENSNLEG00000001982	1 retrocopy	retro_nleu_996,
Pan troglodytes	ENSPTRG00000009579	1 retrocopy	retro_ptro_172,
Ictidomys tridecemlineatus	ENSSTOG00000012903	1 retrocopy	retro_itri_104 ,