RetrogeneDB ID: retro_itri_674

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393310.1:3179435..3180046(+)
• Located in intron of: ENSSTOG00000004849

Retrocopy information

• Ensembl ID: ENSSTOG00000027123
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000023525
• Aliases: None
• Description: None

Sequence

>retro_itri_674
GCTGAGGCTGAGGTAGCCTCCTTGAACCGAAGGATCCAACTGGTTGAAGAGGAGCTGGACCGTGCTCAGGAGCGCCTTGC
TACTACCCTGCAAAAGTTGGAGGAAGCAGAAAAAGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTTATTGAAAACCGGC
CCTAAAAGATGAAGAAAAGATGGAACTCCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGAAGAAGAAGATAGGA
AGTATGAAGAGGTGGCTCGTGAGTTAGTGATTATTGAAGGAGACTTGGAACGCACAGAGGAACGAGCTGAGCTGGCAGAG
TCCCGTTGCCGAGAGATGGATGAGCAGATCAGACTGATGGACCAGAACCTGAAGTGTCTGAATGCTGCTGAAGAAAAGTA
CTCTCAAAAAGAAGACAAATATGAGGAAGAAATAAAGATTCTCACTGATAAACTCAAGGAGGCAGAGACCAGCGCTGAGT
TTGCCCAGAGATCGGTAGCCAAACTGGAAAAGACAATTGATGATTTGGAAGATAAGCTGAAATGCACCAAAGAGGAGCAC
CTCTGTACACAAAGGATGCTGGACCAGACTCTGCTTGACCTGAATGAGATG

Alignment

ORF - retro_itri_674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEAEVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERCMKVIENR-ALKDEEKMELQEIQLK
          AEAEVASLNRRIQLVEEELDRAQERLAT.LQKLEEAEKAADESER.MKVIENR.ALKDEEKMELQEIQLK
Retrocopy AEAEVASLNRRIQLVEEELDRAQERLATTLQKLEEAEKAADESERGMKVIENR<ALKDEEKMELQEIQLK

Parental  EAKHIAEEADRKYEEVARKLVIIEGDLERTEERAELAESRCREMDEQIRLMDQNLKCLNAAEEKYSQKED
          EAKHIAEE.DRKYEEVAR.LVIIEGDLERTEERAELAESRCREMDEQIRLMDQNLKCLNAAEEKYSQKED
Retrocopy EAKHIAEEEDRKYEEVARELVIIEGDLERTEERAELAESRCREMDEQIRLMDQNLKCLNAAEEKYSQKED

Parental  KYEEEIKILTDKLKEAETRAEFAERSVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          KYEEEIKILTDKLKEAET.AEFA.RSVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
Retrocopy KYEEEIKILTDKLKEAETSAEFAQRSVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM

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_674 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_674 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 9 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
Gorilla gorilla	ENSGGOG00000012668	3 retrocopies	retro_ggor_1239, retro_ggor_1817, retro_ggor_2621,
Nomascus leucogenys	ENSNLEG00000010990	8 retrocopies	retro_nleu_1133, retro_nleu_2050, retro_nleu_2119, retro_nleu_2141, retro_nleu_2387, retro_nleu_2523, retro_nleu_921, retro_nleu_922,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230, retro_pabe_3263,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Sus scrofa	ENSSSCG00000006556	3 retrocopies	retro_sscr_318, retro_sscr_604, retro_sscr_781,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674 , retro_itri_709,
Ictidomys tridecemlineatus	ENSSTOG00000024252	1 retrocopy	retro_itri_1858,