RetrogeneDB ID: retro_itri_582

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393303.1:6499145..6499938(+)
• Located in intron of: ENSSTOG00000013729

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000007144
• Aliases: None
• Description: None

Sequence

>retro_itri_582
GCATTTGTACAAGGTACAGTAGCAGAAGGAGTTCCCAGTATTCCATTTTCTGTTCAGCTGAAATACAATATTGAAGTCAT
CTGTGAGTATACATAGTAAAGAAAATACCAGTACCCCCAAAAGACTTTACTTCAGAACCCTGACCTTATTATTAGGTCAT
TTGATGTTAACAGGCCTGGTTGTGAAGTTGACGACCTTAAGGGAGATGTTGCTGGTGGTAGTATTTATTCCAAAAGAAGT
ATTAAAGGTGGGCCAGGAGATAGAAGTCAGACCTGGTATTGTTTCCAAAGACAGTGAAGGAAAACTCATGTGTAAACCAA
TCTTTTCCAAAATTGTATCCCTTTTTATCAAACATAATGATCTTCAGTATGCTGCTCCAGGGGGTCTTACTGGAGTTGGA
ACAAAAATTGTCCCCACTTTGTGCCATGCTGACAGAATGGTGGGGCAGATACTTGGTGCTGTTGGAGCTTTACCTGAGAT
TTTCACAAAATTGTAAATTTCCTATTTCCTGCTTAAACGACTTCTAGGTGTATGCACTGATGGAGACAAGAAAACAGCAA
AAGTCCAAAAACTTTCTATGAATGAAGTGCTCATGGTGAACAAAGGATCACTGTCAACAGGAGGGAGAGTTAGTGCTGTC
AATGCTGATTTGGGCAAAATTGTTTTGACTAATCCTGTGTGCACAGTAGTAGGAGAAAAGATTGCCCTTAGCCAAAGAGT
TGAGAAACACTGGTATTTAATTGGTTGGGGTCAAGTAAGAGGAGTGACAATCAAGCCAACCATAGACGATGAC

Alignment

ORF - retro_itri_582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.9 %
• Parental protein coverage: 55.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFVQGTVAEGAPIIPISAQLKYNIEVVCEYI-VKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGG
          AFVQGTVAEG.P.IP.S.QLKYNIEV.CEY....K...P.......P.LI.IRSFDVN.PGCEVDDLKG.
Retrocopy AFVQGTVAEGVPSIPFSVQLKYNIEVICEYT**RKYQYPQKTLLQNPDLI-IRSFDVNRPGCEVDDLKGD

Parental  VAGGSIL-KGVLKVG-QEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDP
          VAGGSI..K...K.G.QEIEVRPGIVSKDSEGKLMCKPIFSKIVSLF..HNDLQYAAPGGL.GVGTKI.P
Retrocopy VAGGSIYSKRSIKGG>QEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFIKHNDLQYAAPGGLTGVGTKIVP

Parental  TLCRADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGG
          TLC.ADRMVGQ.LGAVGALPEIFT.L.ISYFLL.RLLGV.T.GDKK.AKVQKLS.NEVLMVN.GSLSTGG
Retrocopy TLCHADRMVGQILGAVGALPEIFTKL*ISYFLLKRLLGVCTDGDKKTAKVQKLSMNEVLMVNKGSLSTGG

Parental  RVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD
          RVSAV.ADLGKIVLTNPVCT.VGEKIALS.RVEKHW.LIGWGQ..RGVTIKPT.DDD
Retrocopy RVSAVNADLGKIVLTNPVCTVVGEKIALSQRVEKHWYLIGWGQV-RGVTIKPTIDDD

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_582 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_582 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Mus musculus	ENSMUSG00000035150	2 retrocopies	retro_mmus_1408, retro_mmus_3433,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Ictidomys tridecemlineatus	ENSSTOG00000007144	1 retrocopy	retro_itri_582 ,