RetrogeneDB ID: retro_itri_1224

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393406.1:4689004..4689519(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP12
• Ensembl ID: ENSSTOG00000025153
• Aliases: None
• Description: dual specificity phosphatase 12 [Source:HGNC Symbol;Acc:3067]

Sequence

>retro_itri_1224
GCAGGCATCAGTCGAAGTGTTGCTATAGTGACTGCTTTTTGATGAAGACTGACCGCCTTACCTTTGAAAAAGCCTATGAG
AATCTACAGACTATCAAACCTGGAGCTAAGATGAATGAGGGGTTTGAATATCAACTGGAATCATACCAGGCAATGGGATA
TGAAGTGGGTGCCTCCAGTGCGATTTATAAGCAATATCGCTTACAAAAGTTCACAGACAAGTATCCAGAACTGCACAATC
TACCTCAAGAACTCTTTGCTGTTGATCCAACTACCATTTCACAAGGATTAAAAGATGAAGTTCTCTACAAATGTAGAACA
TGCAGGCGATCCTTATTTCGAAGTTCTAGCATTTTGGATCATAACCAAGGAAGCAGGCCTCTAGCCTTTGCCCACAAGAG
AATGACACCCTCTTTCCTGCTTGCCACAGGGAATCGGGCTCAATGTACATCTTATTTCATTGAACCTGTACAGTGGATGG
AATCCACTTTGTTGGGAGTGATGGACGGGCAGGTG

Alignment

ORF - retro_itri_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.33 %
• Parental protein coverage: 50.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGISRSVAIVTAF-LMKTDRLTFEKAYENLQTIKPEAKMNEGFEYQLKLYQAMGYEVDTSSAIYKQYRLQ
          AGISRSVAIVTAF.LMKTDRLTFEKAYENLQTIKP.AKMNEGFEYQL..YQAMGYEV..SSAIYKQYRLQ
Retrocopy AGISRSVAIVTAF<LMKTDRLTFEKAYENLQTIKPGAKMNEGFEYQLESYQAMGYEVGASSAIYKQYRLQ

Parental  KVTEKYPELQNLPQELFAVDPTTISQGLKDEVLYKCRKCRRSLFRSSSILDHNEGSRPIAFAHKRMTPSF
          K.T.KYPEL.NLPQELFAVDPTTISQGLKDEVLYKCR.CRRSLFRSSSILDHN.GSRP.AFAHKRMTPSF
Retrocopy KFTDKYPELHNLPQELFAVDPTTISQGLKDEVLYKCRTCRRSLFRSSSILDHNQGSRPLAFAHKRMTPSF

Parental  MLATGNQAQCTSYFIEPVQWMESTLLGVMDGQL
          .LATGN.AQCTSYFIEPVQWMESTLLGVMDGQ.
Retrocopy LLATGNRAQCTSYFIEPVQWMESTLLGVMDGQV

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_1224 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1224 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
Otolemur garnettii	ENSOGAG00000000590	1 retrocopy	retro_ogar_2517,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365,
Ictidomys tridecemlineatus	ENSSTOG00000025153	1 retrocopy	retro_itri_1224 ,
Tupaia belangeri	ENSTBEG00000015805	1 retrocopy	retro_tbel_3726,