RetrogeneDB ID: retro_itri_1813

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393868.1:254647..255320(+)
• 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_1813
TCAGTCCTGCTGTTGCCCCATGCACATGCCCTGGACGCTGCAGGCCTGACAAAGAACCTGGGGCTCCACCACCGTGGCTC
ACCAGATGGAAGAGGTGCAGAACGTCAACCCACACCTGTTTGGGCCTGATCAGACTGTAATTCGCAAAGGTCTCATTTTC
CAAGACTAAGAATCCCCTGGGTCTCCCTTGTCAGAAGGAGCTAGTGGTAGCCATGATGAATCCCTTGAAGTCTTCTGCTC
TGTTCTGGGAAGACTGTCTCTCTTCAGCTCCACATCCAAATATAAGTGACTGTGGCTGCAGTGCAGAGGCGATTGTTACC
TTCTGAATGCTTAAATGCCTCGCTGCTGGGAGGTGTTCTCAGAAAAGCAAAGTCCAAAAATGGCTGATCTTTGCAGGAAA
AGTTGGACAAGACTGGGCTGAATCTTCCAGCTGGGAGACGGAAAGCTGCTCTTGTATCCCTCCTGACATCCTTGGTGGAA
GGAAAAGCTGTTAACTTGGCTTGGGACTTTGCATATGTCTGTGAAGTTGAGTTTCCTAGAAAGCCAGTAGCTGGAACATT
TAACCAGGCCTCACCTAGTGGGGTAAAGCAAGATGGAAATGAGGAAGAACAACGCTGCACTTCGGGCAGCTCAGCAAGTG
TGTAAAGAATTCACGGAACTCCTCAATCAAGAC

Alignment

ORF - retro_itri_1813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 60.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SDLLLPHAHALDAAGLAENLGLHD-MAHQMEEVQNVDDPHLLGPDQTVIRKGPI-SMTKNPLGLPCQKEL
          S.LLLPHAHALDAAGL..NLGLH...AHQMEEVQNV..PHL.GPDQTVIRKG.I.S.TKNPLGLPCQKEL
Retrocopy SVLLLPHAHALDAAGLTKNLGLHH>VAHQMEEVQNVN-PHLFGPDQTVIRKGLI>SKTKNPLGLPCQKEL

Parental  VGAVMNPS-EVFCSVPGRLSLLSSTSKYK-VTVAEVQRRLSPPECLNASLLGGVLRRAKSKNGGRSLREK
          V.A.MNP..EVFCSV.GRLSL.SSTSKYK.VTVA.VQRRL.P.ECLNASLLGGVLR.AKSKNG..SL.EK
Retrocopy VVAMMNPL<EVFCSVLGRLSLFSSTSKYK<VTVAAVQRRLLPSECLNASLLGGVLRKAKSKNG*-SLQEK

Parental  LDKIGLNLPAGRRKAAHVTLLTSLVEGEAVHLARDFAYVCEAEFPSKPVA-EYLTRPHLGGRNEMATRKN
          LDK.GLNLPAGRRKAA.V.LLTSLVEG.AV.LA.DFAYVCE.EFP.KPVA.E.LTRPHL.G...M..RKN
Retrocopy LDKTGLNLPAGRRKAALVSLLTSLVEGKAVNLAWDFAYVCEVEFPRKPVA>EHLTRPHLVG*SKMEMRKN

Parental  --TLLAAQQVCKEFTDLLNQD
          ...L.AAQQVCKEFT.LLNQD
Retrocopy NAALRAAQQVCKEFTELLNQD

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_1813 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1813 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,