RetrogeneDB ID: retro_itri_651

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393309.1:4621514..4621824(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD3
• Ensembl ID: ENSSTOG00000025674
• Aliases: None
• Description: small nuclear ribonucleoprotein D3 polypeptide 18kDa [Source:HGNC Symbol;Acc:11160]

Sequence

>retro_itri_651
GGCCACACTGTGTCATGTGAGATGAACATCAGTGAGGTATATCAAGGGAAGTTCAGTGAAGGGGAGGACAATATGAACTG
CCAGATGTTCAACATCACAGTCATGTACAGAGATGGCAGAGTAGTACAACTGGAATAGGCATACATCTGTGACAGCAAGA
TCTGCTTTCTGATTTTGCCTGACAGGCTGAAAACTGCACCCATGTCAAAGAGGATGAAAAATAAAAAGCCAAGATGCAGG
GGCTGGCCAGGGGAAAACTGCTATTCTGAAGGCTCAAGTGGCTACAAGAGGAACAAGATGTGAAATGGGA

Alignment

ORF - retro_itri_651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 81.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNAPMLK
          GH.V.CE.N..EVY.GK..E.EDNMNCQM.NITV.YRDGRV.QLE..YI..SKI.FLILPD.LK.APM.K
Retrocopy GHTVSCEMNISEVYQGKFSEGEDNMNCQMFNITVMYRDGRVVQLE*AYICDSKICFLILPDRLKTAPMSK

Parental  SMKN-KNQGSGAGRGKAAILKAQVAARGRGRGMG
          .MKN.K.Q..GAG.GK.AILKAQVA.RG....MG
Retrocopy RMKN>KSQDAGAGQGKTAILKAQVATRGTRCEMG

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_651 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_651 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013864	1 retrocopy	retro_cfam_173,
Cavia porcellus	ENSCPOG00000012304	1 retrocopy	retro_cpor_297,
Dipodomys ordii	ENSDORG00000005801	1 retrocopy	retro_dord_791,
Ictidomys tridecemlineatus	ENSSTOG00000025674	1 retrocopy	retro_itri_651 ,