RetrogeneDB ID: retro_itri_341

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:28959956..28960429(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM97
• Ensembl ID: ENSSTOG00000007542
• Aliases: None
• Description: transmembrane protein 97 [Source:HGNC Symbol;Acc:28106]

Sequence

>retro_itri_341
ACTGTGATCATCAGGCACAGCCTTGACTTGCTGCTGAACTTCTACTTCCACATCCCCATCACTGTTTTTTGGACCTGCAT
GCCGGTGGTGCTGCCACAAGAATTCTACTGGATCATATTTAGAAACCTGCTAACTTGGTATGCTAAAGAGTTCAAAGACC
CTCTGATATAGAGCACCCAGTATGATTTAAGTCCTTCATGTTTTGTGAGCTTTTGTTTCAGCTGCCTTTCTTTCCCATTA
AACATACACCTTCTTCAAAGGAAATTGCAAGTGGATCCACATTCTTGTAATCATCTACTCAGTTCACATCCTAACAACAT
TAATTCCAATTCTCTCCACATTTCTATTTGGGGATTTCTCCAAAGCCAGTGGTTTCAAAGGACTAGGTTCTGAGACTTTC
CGTGAATGAATAACCTCTTAGCCATCTATACCCCAACAGCCTCATTCCCCTTATACTTCTGGTTTTCATGTTG

Alignment

ORF - retro_itri_341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.88 %
• Parental protein coverage: 91.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TMIVKRSIDFLLGFYFLSHIPITLFLD-LQVVLPRQLYSVKLRNLLAWYAEEFKDPLIQST-PVWFQSFV
          T.I...S.D.LL.FYF..HIPIT.F.....VVLP...Y....RNLL.WYA.EFKDPLI.ST.PV.F.SF.
Retrocopy TVIIRHSLDLLLNFYF--HIPITVFWTCMPVVLPQEFYWIIFRNLLTWYAKEFKDPLI*ST<PV*FKSFM

Parental  FCELLFQLPFFPAA-TYAFFKGNCKWIRMPAIIYSVHTLTTLIPILSTFLFGDFSKASGFKGVGPESFHE
          FCELLFQLPFFP...TY.FFKGNCKWI....IIYSVH.LTTLIPILSTFLFGDFSKASGFKG.G.E.F.E
Retrocopy FCELLFQLPFFPIK<TYTFFKGNCKWIHILVIIYSVHILTTLIPILSTFLFGDFSKASGFKGLGSETFRE

Parental  RIT-LMAIYA-PYFIVPFILLLFML
          .IT.L.AIY..P....P.ILL.FML
Retrocopy *IT<LLAIYT<PNSLIPLILLVFML

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_341 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_341 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011105	1 retrocopy	retro_chof_566,
Homo sapiens	ENSG00000109084	1 retrocopy	retro_hsap_4027,
Gorilla gorilla	ENSGGOG00000004565	1 retrocopy	retro_ggor_2703,
Macaca mulatta	ENSMMUG00000019142	1 retrocopy	retro_mmul_2323,
Mus musculus	ENSMUSG00000037278	1 retrocopy	retro_mmus_1451,
Nomascus leucogenys	ENSNLEG00000001868	1 retrocopy	retro_nleu_1574,
Otolemur garnettii	ENSOGAG00000003329	1 retrocopy	retro_ogar_1913,
Pongo abelii	ENSPPYG00000008086	1 retrocopy	retro_pabe_3307,
Pan troglodytes	ENSPTRG00000008909	1 retrocopy	retro_ptro_2731,
Ictidomys tridecemlineatus	ENSSTOG00000007542	2 retrocopies	retro_itri_341 , retro_itri_758,
Tupaia belangeri	ENSTBEG00000005125	2 retrocopies	retro_tbel_2160, retro_tbel_2221,