RetrogeneDB ID: retro_itri_1391

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393470.1:3622501..3622939(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: B4GALT6
• Ensembl ID: ENSSTOG00000010911
• Aliases: None
• Description: UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6 [Source:HGNC Symbol;Acc:929]

Sequence

>retro_itri_1391
ATGCTAGCATTTCTCAGTGCCAATGTAAGCAAGGTCAGTTTTGGTGAAGTTCATCATTTCTTCTCTAATGATTTGGATAT
TGAGCCAGGAGGTCACTGGAGGCTAAAGGACTGTAAACACAGATGGAAGGTGACAGTTCTCATTCCCCTCCACAACCACC
ATGAACAGCTTCTGTGTTTTTTTTTCTTATATTTGTTTTCAATGTTTCAGAAACAGTACCTGGAATTTGCCTTTTATGTC
ATTGAACAGACTGGCACACAATCTTTTAATCATGCTGTGCTCTTCTACATGGGCTTCAAGGAGGCCATGAAAGACAACAT
CTAGGACTGTGTGATCTTCCATGATGTGCATCATCTACCTGAAAATGAGGGAAACTATTATGGATGTGGAAAAATGCCTT
GTCACTTTGTAGCAGAGATGGATAAATACATGTATGTA

Alignment

ORF - retro_itri_1391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.92 %
• Parental protein coverage: 54.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRGFLSVNVSEVSFDEVHQLFSKDLDIEPGGHWRPKDCKPRWKVAVLIPFRNRHEHL-PIFFLHLIPMLQ
          M..FLS.NVS.VSF.EVH..FS.DLDIEPGGHWR.KDCK.RWKV.VLIP..N.HE.L.....L.L..M.Q
Retrocopy MLAFLSANVSKVSFGEVHHFFSNDLDIEPGGHWRLKDCKHRWKVTVLIPLHNHHEQLLXXXXLYLFSMFQ

Parental  KQRLEFAFYVIEQTGTQPFNRAMLFNVGFKEAMKDNVWDCVIFHDVDHLPENDRNYYGCGEMPRHFAAKL
          KQ.LEFAFYVIEQTGTQ.FN.A.LF..GFKEAMKDN..DCVIFHDV.HLPEN..NYYGCG.MP.HF.A..
Retrocopy KQYLEFAFYVIEQTGTQSFNHAVLFYMGFKEAMKDNI*DCVIFHDVHHLPENEGNYYGCGKMPCHFVAEM

Parental  DKYMYI
          DKYMY.
Retrocopy DKYMYV

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_1391 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1391 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020816	1 retrocopy	retro_cjac_1251,
Ictidomys tridecemlineatus	ENSSTOG00000010911	1 retrocopy	retro_itri_1391 ,
Tetraodon nigroviridis	ENSTNIG00000010472	1 retrocopy	retro_tnig_6,
Takifugu rubripes	ENSTRUG00000005726	1 retrocopy	retro_trub_9,