RetrogeneDB ID: retro_itri_403

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:4172311..4173021(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIP4K2B
• Ensembl ID: ENSSTOG00000014263
• Aliases: None
• Description: phosphatidylinositol-5-phosphate 4-kinase, type II, beta [Source:HGNC Symbol;Acc:8998]

Sequence

>retro_itri_403
TTGCCACAGTACCTGGGCATGTACTGCCTGACTGTGAACATAGTGGAAACTTACATGGTGGTCCAAAGGAATATGTTTAG
CCATCAGCTCACTGCACTTGGCAAGTATGACCTCAAGGATTCTACTGTTGCCAGAGAAACAAGTGACAAAGGCAAGGCCA
AGTACTTTCAACACTCAAAGACAATGACTTCCTCAATGAAGGACAGAAGCTGCATGTAGGAGAGGAGAGTAAATAGAACT
TCCTGGAGAAACTGAAGTAGGACATTGAGTTCCTGGCCCAGATAAAGACAACTGACTACAACCTGCTGGTGGACATCCAA
GATGTGGACTGGGAGGAACAGGAGGAGATGGAGGTGGAAGAACAAGAAGAAGACAAAGAAAGTGTGAATGATGGGGTGGG
CAGTAACCTGTTTTGCTCCTATGGCATACATCCGGACAGCCCTGGTAACCTCCTCAGCTTTCCCCTGTTCTTTGGTCCTA
GGGAGTTCAACCCCTCTGTTGATGTCCATGCCATGAAAATCCATGAAAGTACCCCCAAGAAGGTGGTCTATTTCATGGCC
ATCATCAACATCTTCATGCCTTATGATCCTAAGAAGAAAGTTGCACACACCACCAAAACAATGAAGCATGGGGTACAGGC
TGAGATCTTGACTGTGAACCCCAAGTAGTAGTCCAAACATTTCAATGAATTCATGTCCAAGATCTTGACA

Alignment

ORF - retro_itri_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.21 %
• Parental protein coverage: 64.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPQFLGMYRLTVDGVETYMVVTRNVFSHRLTVHRKYDLKGSTVAREASDKEKAKD-LPTFKDNDFLNEGQ
          LPQ.LGMY.LTV..VETYMVV.RN.FSH.LT...KYDLK.STVARE.SDK.KAK..L.T.KDNDFLNEGQ
Retrocopy LPQYLGMYCLTVNIVETYMVVQRNMFSHQLTALGKYDLKDSTVARETSDKGKAKY<LSTLKDNDFLNEGQ

Parental  KLHVGEESKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRAEQEEMEVEERAEDEECENDGVGSNLLC
          KLHVGEESK.NFLEKLK.D.EFLAQ.K..DY.LLV.I.DVD..EQEEMEVEE..ED.E..NDGVGSNL.C
Retrocopy KLHVGEESK*NFLEKLK*DIEFLAQIKTTDYNLLVDIQDVDWEEQEEMEVEEQEEDKESVNDGVGSNLFC

Parental  SYGTPPDSPGNLLSFPRFFGPGEFDPSVDVYAMKSHESAPKKEVYFMAIIDILTPYDAKKKAAHAAKTVK
          SYG..PDSPGNLLSFP.FFGP.EF.PSVDV.AMK.HES.PKK.VYFMAII.I..PYD.KKK.AH..KT.K
Retrocopy SYGIHPDSPGNLLSFPLFFGPREFNPSVDVHAMKIHESTPKKVVYFMAIINIFMPYDPKKKVAHTTKTMK

Parental  HGAGAEISTVNPEQYSKRFNEFMSNILT
          HG..AEI.TVNP...SK.FNEFMS.ILT
Retrocopy HGVQAEILTVNPK**SKHFNEFMSKILT

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_403 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_403 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sorex araneus	ENSSARG00000013917	1 retrocopy	retro_sara_644,
Ictidomys tridecemlineatus	ENSSTOG00000014263	1 retrocopy	retro_itri_403 ,