RetrogeneDB ID: retro_itri_1801

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393830.1:26802..27533(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAP2C
• Ensembl ID: ENSSTOG00000014299
• Aliases: None
• Description: transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) [Source:HGNC Symbol;Acc:11744]

Sequence

>retro_itri_1801
GCTGGCCTGCTTCCCCAACTCTCTAGGATAGAGGGAGGTGCTGTAGGCGCCCTCGGGGATGCTAACAGCTGCTCAGACTT
ACTGTTACCCCATGGCATGCCCTGGATGCTGCAGGCCTGGCAAAGTACCTGGGGCTCCATGACATGGCTCACCAGATGAA
AGAGGTGCAGAATGTCAACCTGCTTGGGCCTGATCAGTCTGTAATCTGCAAAAGTCCGATTTTCCATGGCTAAGAACCCC
CTGGGTCTCCCCTGTCAGGAGGATCTGGTGGTAGCCCTGATGAATCCCATGAAGTCTTCTGCTTGGTTCTGGGAAGACTG
TCTCTCTTCAGCTCCATGTCCAAATATAAGTGACTGTGGCTGAAGTGCAGAGGCAATTGTCACCTTCTGAATGCTTAAAT
GCCTCACTGCTGGGAGATGTTCTCAGGAAAGCAAAGTCCCAAAATGACTGATTGTTGTGGGAAAAGTTGGACAAGACTGG
GCTAGATCTTCAAGCTGGAATATGGAAAGCTGCTCTTGTGACCACCCTGACATCCTTGGTGGAAGAAAAAGCTGTTCACT
TGGCTGGGTACTTTGCATATGGCTGTGAACTGAAGTTTCCTAGTAAGCCAGTGGCCAAATATTTAACCAGGCCTCACCTA
GGAGGGTAAATTAAGATGGTAACAAGGAAGAATAATGCTGTGGGTGTCTCAGCAAGTGTGTAAAGAATTCATGGACCCCC
TCAATTAAGAC

Alignment

ORF - retro_itri_1801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.94 %
• Parental protein coverage: 67.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ASLLPHLSGLEGGAVGARRDAYRRSDLLLPHA-HALDAAGLAENLGLHDMAHQMEEVQNVDDPHLLGPDQ
          A.LLP.LS..EGGAVGA..DA...SDLLLPH..HALDAAGLA..LGLHDMAHQM.EVQNV....LLGPDQ
Retrocopy AGLLPQLSRIEGGAVGALGDANSCSDLLLPHG<HALDAAGLAKYLGLHDMAHQMKEVQNVN---LLGPDQ

Parental  TVIRKGPI-SMTKNPLGLPCQKELVGAVMNPS-EVFCSVPGRLSLLSSTSKYK-VTVAEVQRRLSPPECL
          .VI.K.PI.SM.KNPLGLPCQ..LV.A.MNP..EVFC.V.GRLSL.SS.SKYK.VTVAEVQR.LSP.ECL
Retrocopy SVICKSPI>SMAKNPLGLPCQEDLVVALMNPM<EVFCLVLGRLSLFSSMSKYK<VTVAEVQRQLSPSECL

Parental  NASLLGGVLRRAKSKNGGRSLREKLDKIGLNLPAGRRKAAHVTLLTSLVEGEAVHLARDFAYVCEAEFPS
          NASLLG.VLR.AKS.N....L.EKLDK.GL.L.AG..KAA.VT.LTSLVE..AVHLA..FAY.CE..FPS
Retrocopy NASLLGDVLRKAKSQND*L-LWEKLDKTGLDLQAGIWKAALVTTLTSLVEEKAVHLAGYFAYGCELKFPS

Parental  KPVAEYLTRPHLGGRNEMATRKNT-LLAAQQVCKEFTDLLNQD
          KPVA.YLTRPHLGG...M.TRKN..L...QQVCKEF.D.LN.D
Retrocopy KPVAKYLTRPHLGG*IKMVTRKNN>LWVSQQVCKEFMDPLN*D

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_1801 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1801 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011025	1 retrocopy	retro_chof_1226,
Macropus eugenii	ENSMEUG00000007703	1 retrocopy	retro_meug_166,
Myotis lucifugus	ENSMLUG00000010003	2 retrocopies	retro_mluc_284, retro_mluc_5,
Monodelphis domestica	ENSMODG00000016445	1 retrocopy	retro_mdom_728,
Otolemur garnettii	ENSOGAG00000033901	1 retrocopy	retro_ogar_1767,
Pan troglodytes	ENSPTRG00000013654	1 retrocopy	retro_ptro_1933,
Ictidomys tridecemlineatus	ENSSTOG00000001781	1 retrocopy	retro_itri_1860,
Ictidomys tridecemlineatus	ENSSTOG00000014299	3 retrocopies	retro_itri_1741, retro_itri_1801 , retro_itri_1813,
Tursiops truncatus	ENSTTRG00000005983	1 retrocopy	retro_ttru_535,