RetrogeneDB ID: retro_itri_1379

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393466.1:1600113..1601187(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUMB
• Ensembl ID: ENSSTOG00000003900
• Aliases: None
• Description: numb homolog (Drosophila) [Source:HGNC Symbol;Acc:8060]

Sequence

>retro_itri_1379
TCCCTTTGCATCAATGAGTTGCCTTCCACTATGCAGAGGAAGACTGATTTCCCCATAAAAAATGCAGTGCCAGAGGTAGA
AGGGGAGGCAGAGAGCATCAGTTCCCTGTGCTCACAGATCACCAATGTCTTCAGCACACCCTCTGAGGACCCCCTCTCTT
CCGCCCCAATGACCAAACCAGTGACAGTGGTGGCATCACAGTCTCCTGCCTTCCAAGCTAATGGCACTGACTCAGCCTTC
CATGTGCTTGCTGCTAAGCCAGTCCATACTGCTCTAGCACCCGTAGCAATGCCTGTGCTTGAAACCAACCCTTGGGCCCA
TGCCCCTGATGCTAACAAGGAAATTGCAGCCATTCACCCTGGGACTGAGTGGGGTCAGTCTTCTGGTGCTGCATCTCCAG
GTCTCTTCCATGGTGGTCACAGACGTACTCCCTCTGAGGCTGACCGATGGTTAGAAGAAGTGTCGAAGAGTCTCTGAGCC
CAGCAGCCCCAGGTCTCAGCTGCCCCTTTGCAGCCAGTTCTCCAGCCTCCTCCACCCACTGCCATTTCCCAGCCAGCACC
GCCTTTCCAAGGGAATGCATTCCTCACCTCTCAGCCTGTGCCAGTGGGTGTGGTCCCAACCCTGCAGCCAACCTTTGTCC
CTACCCAGTCCTATCCTGTGGCCAATGGGATGTCCTATCCAGCCCCTAATGTGCCTATGGTGGGCATCACTCTCTCCCAG
ATGGTAGCCAATGTGTTTGGCACTGCAGGCCATCCTCAGGCCACTCATCCCCATCCATCTCCCAGCCTGGTCAAGCAACA
GACATTCCCACAGTATGAGACAAGCAGTGCTACCACCAGTCTCTTCTTTAAGCCTCCTGCTCAGCACCTCAACGGTTCTG
CAGCTTTCAATGGTGTAGATGATGGCAGGTTGGCCTCAGGAGACAAGCACACAGAGGTTCCTGCAGGCACCTGCCCAGTG
GATCCTTTTGAAGCTCAGTGGGCTGCATTAGAAAGCAAATCCAAGCAGTGTACTAATCCCTCCCCTACCAACCCATTTTC
CAGTGACTTACAGAAGACATTTGAAACTGAACTT

Alignment

ORF - retro_itri_1379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.26 %
• Parental protein coverage: 59.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLRINELPSTMQRKTDFPIKNAVPEVEGEAESISSLCSQITNAFSTPSEDPFSSAPMTKPVTVVAPQSPA
          SL.INELPSTMQRKTDFPIKNAVPEVEGEAESISSLCSQITN.FSTPSEDP.SSAPMTKPVTVVA.QSPA
Retrocopy SLCINELPSTMQRKTDFPIKNAVPEVEGEAESISSLCSQITNVFSTPSEDPLSSAPMTKPVTVVASQSPA

Parental  FQANGTDSAFHVLAAKPVHTALAPVAMPVRETNPWANAPDAANKEIAAIHPGTEWGQSSGAASPGLFHGG
          FQANGTDSAFHVLAAKPVHTALAPVAMPV.ETNPWA.APDA.NKEIAAIHPGTEWGQSSGAASPGLFHGG
Retrocopy FQANGTDSAFHVLAAKPVHTALAPVAMPVLETNPWAHAPDA-NKEIAAIHPGTEWGQSSGAASPGLFHGG

Parental  HRRTPSEADRWLEEVSKSVRAQQPQVSAAPLQPVLQPPPPTAISHPAPPFQGNAFLTSQPVPVGVVPPLQ
          HRRTPSEADRWLEEVSKS..AQQPQVSAAPLQPVLQPPPPTAIS.PAPPFQGNAFLTSQPVPVGVVP.LQ
Retrocopy HRRTPSEADRWLEEVSKSL*AQQPQVSAAPLQPVLQPPPPTAISQPAPPFQGNAFLTSQPVPVGVVPTLQ

Parental  PTFVPAQSYPVANGMSYPAPNVPVVGITPSQMVANVFGTAGHPQATHPHPSPSLVKQQTFPQYETSSATT
          PTFVP.QSYPVANGMSYPAPNVP.VGIT.SQMVANVFGTAGHPQATHPHPSPSLVKQQTFPQYETSSATT
Retrocopy PTFVPTQSYPVANGMSYPAPNVPMVGITLSQMVANVFGTAGHPQATHPHPSPSLVKQQTFPQYETSSATT

Parental  SPFFKPPAQHLNGSAAFNGVDDGRLASGDKHTEVPAGTCPVDPFEAQWAALESKSKQRTNPSPTNPFSSD
          S.FFKPPAQHLNGSAAFNGVDDGRLASGDKHTEVPAGTCPVDPFEAQWAALESKSKQ.TNPSPTNPFSSD
Retrocopy SLFFKPPAQHLNGSAAFNGVDDGRLASGDKHTEVPAGTCPVDPFEAQWAALESKSKQCTNPSPTNPFSSD

Parental  LQKTFEIEL
          LQKTFE.EL
Retrocopy LQKTFETEL

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_1379 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1379 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000003900	1 retrocopy	retro_itri_1379 ,