RetrogeneDB ID: retro_itri_1367

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393459.1:3499240..3499775(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN13
• Ensembl ID: ENSSTOG00000008833
• Aliases: None
• Description: tetraspanin 13 [Source:HGNC Symbol;Acc:21643]

Sequence

>retro_itri_1367
ATTGGATTTGCTGCTAGAGGCATTTGCTTTGGACTGATATATAGTCACCAAGTGGCCAGTGTTGTCATTGCATTTGACAT
CTTCATGTTTCTGACTGCATTAGTGGGCTAATTGGAGCTGAGAAACAGCATCAGGTGTTACTATTCCTTTTTAAAAAATA
TATGATTAGTCCCCTCCTTGTATTTATTGTTCAGTTTTCTGTTTGTTGTGCTTGCTTAGCCTGGGATCAGGAGCAACAGT
CAGCTTCTGGAGGGTGGTTGGAATAATACAGCAAGTGTTCAAAATGACATCCAGAGAAACTTAAACTGTTGTGAGTTCTG
AAGTTTTAACCCAAATTACACCTATCTGGCCAGCTGTGTTCAAAAGCAGCCACCAGTGCTTGCTGTGTGCTCTAATAATG
GGAGAATATATTGGGGCGGTTTTGAGATTTTTGGGTGGTCTTGGCCTCTTTTTTTCAGTTTCAGAGATCCTGAGGGTTTG
GATGAACTACAAATATAGGAATCAGAAAGATCCTGGCACTAATCCTACTGCATTC

Alignment

ORF - retro_itri_1367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.33 %
• Parental protein coverage: 86.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IGIAAWGIGFGLISSLRVVGVVIAVGIFLFLIALVG-LIGAVKHHQVLLFF---YMIILLLVFIVQFSVS
          IG.AA.GI.FGLI.S..V..VVIA..IF.FL.ALVG.LIGA.K.HQVLLF....YMI..LLVFIVQFSV.
Retrocopy IGFAARGICFGLIYSHQVASVVIAFDIFMFLTALVG<LIGAEKQHQVLLFLFKKYMISPLLVFIVQFSVC

Parental  CACLALNQEQQ-SQLLEVGWNNTASARNDIQRNLNCCGFRSFNPNDTCLASC-FQSSHKCSLCAPIIGEY
          CACLA.....Q.SQLLE.GWNNTAS..NDIQRNLNCC.F.SFNPN.T.LASC.F.SSH.C.LCA.I.GEY
Retrocopy CACLAWD-QEQ>SQLLEGGWNNTASVQNDIQRNLNCCEF*SFNPNYTYLASC>FKSSHQCLLCALIMGEY

Parental  AGEVLRFVGGIGLFFSFTEILGVWLTYRYRNQKDPRANPSAF
          .G.VLRF.GG.GLFFS..EIL.VW..Y.YRNQKDP..NP.AF
Retrocopy IGAVLRFLGGLGLFFSVSEILRVWMNYKYRNQKDPGTNPTAF

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_1367 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1367 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010524	1 retrocopy	retro_amel_1425,
Choloepus hoffmanni	ENSCHOG00000013574	2 retrocopies	retro_chof_1137, retro_chof_861,
Loxodonta africana	ENSLAFG00000005956	3 retrocopies	retro_lafr_1088, retro_lafr_195, retro_lafr_556,
Ictidomys tridecemlineatus	ENSSTOG00000001138	1 retrocopy	retro_itri_1256,
Ictidomys tridecemlineatus	ENSSTOG00000008833	1 retrocopy	retro_itri_1367 ,
Tursiops truncatus	ENSTTRG00000009870	1 retrocopy	retro_ttru_551,