RetrogeneDB ID: retro_itri_1860

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394226.1:862..1587(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAP2E
• Ensembl ID: ENSSTOG00000001781
• Aliases: None
• Description: transcription factor AP-2 epsilon (activating enhancer binding protein 2 epsilon) [Source:HGNC Symbol;Acc:30774]

Sequence

>retro_itri_1860
CTCTCATTGGCCAAAGACAGCCTGGTTGGCAGCATCACCAGCTCCAGTGAGGTCTTCTGCTCCCTGTCTGGACGGCTTTC
ATTGCTCAGCTCAACATCCAAGTATAAGGTGACCATGGGGGAAGTACAGTTGTGACTCTAACCTCCTGAGTGCCTTAACG
CCTCCCTCCTGGGGGGCATCCTCTGCAGAGTCAAGTCAAAGAATGGGGGTCGTGTCTATAGGAAAGGCTAGAGAAGATTG
GCTCAACCTGCCAGCAGGCTATAGGAAGGCTGCCAATGTGACACTGCTGACCTCACTGGTGGAGGGAGAGTCTGTGCACC
TGAATCAAGACTTTGGCTACATCTGTGAGACTGAGTTCCCAGCCAAAGCAGCTGCTGAGTACCTGTGCTGACAGCATGCT
GACCCCAGGAAACTGCACAGCCACAGAGCATGCTGCTGGCCTCCAAGAAGATCTGCTAGTAGTTTGCGGACTTGATGTCT
CAGGATCGCTCCCCATTGGGCAACAGCCACCCAGCACTCATCCAGGAGCCTGGAGTGCAAAGTCACCTGACACACTTTAG
CCTCATCACCCATGGCTTTGAAGGGCCTGCCATCTATGCTTCCCTCACTGCCTTCCAGAACTATCTGCTGGAGTCACTCA
AGCGACTGGACAAGATGTTTCTAACCAGTGCAGGCAGTGCACATAGTGAAACCAAGGCTTCAGAGAAGGATGCCAACATA
GGAAA

Alignment

ORF - retro_itri_1860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.4 %
• Parental protein coverage: 76.9 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSLAKDSLVGSITNPSEVFCSVPGRLSLLSSTSKYKVTVGEVQRRLSPPECLNASLLGGVLRRAKSKNGG
          LSLAKDSLVGSIT..SEVFCS..GRLSLLSSTSKYKVT.GEVQ..L.PPECLNASLLGG.L.R.KSKNGG
Retrocopy LSLAKDSLVGSITSSSEVFCSLSGRLSLLSSTSKYKVTMGEVQL*L*PPECLNASLLGGILCRVKSKNGG

Parental  R-CLRERLEKIG-LNLPAGRRKAANVTLLTSLVEGEAVHLARDFGYVCETEFPAKAAAEYLCRQHADPGE
          R.CL.ERLEKIG.LNLPAG.RKAANVTLLTSLVEGE.VHL..DFGY.CETEFPAKAAAEYLC.QHADP..
Retrocopy R<CL*ERLEKIG<LNLPAGYRKAANVTLLTSLVEGESVHLNQDFGYICETEFPAKAAAEYLC*QHADPRK

Parental  LHSRK-SMLLAAKQICKEFADLMAQDRSPLGNSRPALILEPGVQSCLTHFSLITHGFGGPAICAALTAFQ
          LHS...SMLLA.K.IC..FADLM.QDRSPLGNS.PALI.EPGVQS.LTHFSLITHGF.GPAI.A.LTAFQ
Retrocopy LHSHR<SMLLASKKIC**FADLMSQDRSPLGNSHPALIQEPGVQSHLTHFSLITHGFEGPAIYASLTAFQ

Parental  NYLLESLKGLDKMFLTSAGSGHGETKASEKDA-KHRK
          NYLLESLK.LDKMFLTSAGS.H.ETKASEKDA..HRK
Retrocopy NYLLESLKRLDKMFLTSAGSAHSETKASEKDA<QHRK

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_1860 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1860 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000001781	1 retrocopy	retro_itri_1860 ,
Ictidomys tridecemlineatus	ENSSTOG00000014299	3 retrocopies	retro_itri_1741, retro_itri_1801, retro_itri_1813,