RetrogeneDB ID: retro_itri_1289

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393429.1:2994762..2996194(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKAP1
• Ensembl ID: ENSSTOG00000022206
• Aliases: None
• Description: A kinase (PRKA) anchor protein 1 [Source:HGNC Symbol;Acc:367]

Sequence

>retro_itri_1289
AGGCAAGAGAGAGGAGCCGAGGGGACCGGTGATGCAATGTTGGGGGAAAACGTGCTTGAAGAAGGCTTGTTGTCCCAGGA
GCGTGTCTCAGAATTGGAGAATAGCAAGGCCCTCAGCCTGGCCCCCTCGGGAGGCAGAGGAGAGAAGGGGAGCGGTGGCC
CCTTCTCCCCTCTGAGAGAAGAGTCTGCAGTTGGAAAATTGTTAAGTAGCTCTGGCAAGTTGGTTCACACAGAGCTGGCA
AAGGATGAGGAGATGCAGGCATCTGAGGTCCAAGATGACAGTACCTGGGACAGAGACATGGCGGCAGAAGTAGGCAAAAA
GGAAAGCTTGGATAAGAATGGGAGATTGAGCAGGCTGCCTTCCAGATAATCTCCCAGGTGATCTTGGAAGCAACCCAAGA
GGTGCTGGCCAGCACAGGGGACAAGATGGCAGATCAGTTATATCAGGCCTCAGACAGTCCGACTGTAGGGCAAGCCGAGA
GCAGTGCCCCAGCCAGCCAGAAAACTGTCCTGGGGCAAGACACTGCACAGGCTGCTCCAGCCGTAGTGGGGGCAGCCGCT
GGTGCAGTGGACTCTGCCCTTCCCTTGCCAGGCCCACCAGCAGAGAACCTGCCTTCACCAAAGACCTATGTGAGCTGCCT
GAGCAGCCCACTGTCCAGCCTCACTGAGGACAGTAAGCCAAAGAACTCCGCACACCACATCTCCCTGGCTCCCTGCCCAC
CTCCAGCGAGCCCCCTCAGAGAGTCCGTGGACGAGGCAAGCATCCTGGTGGAAGATTCCACCTGTGCCACCTGTGTGTCA
GACAGCCAGAGTGTTCCTTCCGCAGCCTCCTCCGGGCAGTGCTTGGATTCTGTCAGCACTTCAGGGCTCGAAGACTCTTG
CACAGAGACCAACTCAAGCCCCAGGGACAAGGCCATCACCCCGCCGCTGTCGGACAATACTGTGCCCTTCAGTAATGGGG
TGCTGAAAGGGGAGTTGTCAGACTTGGGGACTGAGGACGGATGGACTGTGGATGCAGAAACAGATCACTCGGGAGGTTCC
AACTGGGACAGCATGGATTCTGTGGATAGCTGTTGTGGCCTCAAGAAGACCGACAGTTTCCAGAATGCCCAGGCAGGCTC
CAACCCAAAAAAGTTGACCTCATCATCTGGGAGACTGAAGTGCCAAAGCACTTAGTTGGTCGGCTACTCGGCAAGCAGGG
GCGGTATGTGAGTTTCCTGAAGCAAACATCTGGTGCCAAGATCTACATCTCAACCCTGCCTTACACCCAGAACATCCAGA
TCTGCCACATAGAAGGCTCTCGGCATCATGTAGACAAAGCTCTGAATCTGATTAGAAAGAAGTTCAAGGAACTGAATCTC
ACTAATATTTACGCTCCTCTGCTGCTTTCACTGGCACTGCCTTCTCTATCAGTGACGTCCTGGCTCATGCTG

Alignment

ORF - retro_itri_1289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.08 %
• Parental protein coverage: 59.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RETRGAEGTGDAMLGENVLEEGLLSQERVSELENSKALSLAPLGGGGEKGSGGPFSPLREESAVGKLLSS
          R..RGAEGTGDAMLGENVLEEGLLSQERVSELENSKALSLAP.GG.GEKGSGGPFSPLREESAVGKLLSS
Retrocopy RQERGAEGTGDAMLGENVLEEGLLSQERVSELENSKALSLAPSGGRGEKGSGGPFSPLREESAVGKLLSS

Parental  SGKLAHAELAKDEEMQASEVQDDSTWDRDMAAELGKKESLDKNER-IEQAAFQIISQVILEATEEVLAST
          SGKL.H.ELAKDEEMQASEVQDDSTWDRDMAAE.GKKESLDKN.R.IEQAAFQIISQVILEAT.EVLAST
Retrocopy SGKLVHTELAKDEEMQASEVQDDSTWDRDMAAEVGKKESLDKNGR<IEQAAFQIISQVILEATQEVLAST

Parental  GDKMADQLYQASGSPTVGQAESSAPASQKTVLGQDTAQAAPAVVGAASGPVDPALPLPGPPAENLPSPKT
          GDKMADQLYQAS.SPTVGQAESSAPASQKTVLGQDTAQAAPAVVGAA.G.VD.ALPLPGPPAENLPSPKT
Retrocopy GDKMADQLYQASDSPTVGQAESSAPASQKTVLGQDTAQAAPAVVGAAAGAVDSALPLPGPPAENLPSPKT

Parental  YVSCLSSPLSSPTKDSKPKNSAHHISLAPCPPPASPLRESVDEASILAEDATCATCVSASQSVPSAASSG
          YVSCLSSPLSS.T.DSKPKNSAHHISLAPCPPPASPLRESVDEASIL.ED.TCATCVS.SQSVPSAASSG
Retrocopy YVSCLSSPLSSLTEDSKPKNSAHHISLAPCPPPASPLRESVDEASILVEDSTCATCVSDSQSVPSAASSG

Parental  QCSDSVSTSGLEDSCTETNSSPRDKAITPPLPDSTVPFSNGVLKGELSDLGTEDGWTADAEADHSGGSDG
          QC.DSVSTSGLEDSCTETNSSPRDKAITPPL.D.TVPFSNGVLKGELSDLGTEDGWT.DAE.DHSGGS..
Retrocopy QCLDSVSTSGLEDSCTETNSSPRDKAITPPLSDNTVPFSNGVLKGELSDLGTEDGWTVDAETDHSGGSNW

Parental  NSMDSVDSCCGLKKTDSFQNAQAGSN-PKKVDLIIWEIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYIS
          .SMDSVDSCCGLKKTDSFQNAQAGSN.PKKVDLIIWE.EVPKHLVGRL.GKQGRYVSFLKQTSGAKIYIS
Retrocopy DSMDSVDSCCGLKKTDSFQNAQAGSN<PKKVDLIIWETEVPKHLVGRLLGKQGRYVSFLKQTSGAKIYIS

Parental  TLPYTQNIQICHIEGSQHHVDKALNLIGKKFKELNLTNIYAPPLPSLALPSLPMTSWVSL
          TLPYTQNIQICHIEGS.HHVDKALNLI.KKFKELNLTNIYAP.L.SLALPSL..TSW..L
Retrocopy TLPYTQNIQICHIEGSRHHVDKALNLIRKKFKELNLTNIYAPLLLSLALPSLSVTSWLML

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_1289 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1289 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000022206	1 retrocopy	retro_itri_1289 ,