RetrogeneDB ID: retro_itri_115

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393304.1:11466628..11467753(-)
• Located in intron of: ENSSTOG00000011078

Retrocopy information

• Ensembl ID: ENSSTOG00000011088
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000007438
• Aliases: None
• Description: None

Sequence

>retro_itri_115
ATGGATGCCTTGCGACTGGCAAATTCGGCTTTTGCTGTTGACCTGTTCAAACAACTGTGTGAAAAGGAGCCAGTGGGCAA
TGTCCTCTTCTCCCCAATCTGTCTCTCCACTTCTCTGTCACTTGCTCAAGTAGGCGCCAAAGGTGACACAGCAAATGAAA
TTGGACAGGTCCTTCATTTTGACAATGTCAAAGATGTGCCCTTCGGATATCAAACAGTCACCTCGGATGTAAATAAACTC
AGTTCCTTTTACTCTTTGAAACCAATCAAGCGGCTCTACGTAGACAAATCACTGAACCCTTCTACAGAGTTCATCAGCTC
TACAAAGAGACCATATGCAAAAGAATTGGAAACCGTGGACTTCAAGGATAAACTGGAAGAAACGAAAGGTCAGATCAACA
GCTCCATTAAGGATCTCACTGACGGCCACTTTGAGAACATTTTGTCTGACAACAGTGTAAATGACCAGACCAAAATCCTC
GTGGTTAATGCTGCCTACTTTGTTGGAAAGTGGATGAAGAAATTCCCTGAATCAGAAACAAAAGAATGCCCTTTCAGAGT
CAGCAAGACAGACGCCAAGCCTGTGCAGATGATGAACATGGAGGCCACATTCTGTATGGGCAACATTGATGACATCAATT
GCAAGATCATTGAGCTTCCTTTCCAAAATAAGCACCTCAGCATGCTCATCCTGCTACCCAAGGATGTGGAGGATGAGTCG
ATGGGCTTGGAGAAGATTGAAAAACAACTCAACTCAGAGACGCTGTTTCAGTGGACCAATCCCAGCACCATGGCCAATGC
CAAAGTCAAACTCTCCCTTCCCAAGTTTAAGGTGGAAAAGATCATTGACCCAAAGTCTAGTCTGGAAAACCTAGGGCTGA
AAAATACCTTTAACGAAGATACATCTGATTTCTCTGGAATGTCAGAGACCAAGGGAGTGGCCCTGTCGAATGTCATTCAC
AGAGCGTGCTTAGAAATAAATGAAGATGGTGGGGAGTCCATTGAGGTGCCAGGATCCCGGATCCTGCAACACAAGGATGA
ATTTAACGCCGACCACCCATTTATTTACATCATCAGGCACAACAAAACCCGAAACATCATTTTCTTTGGCAAGTTCTGTA
CTCCT

Alignment

ORF - retro_itri_115 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.93 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDALRLANSAFAVDLFKQLCEKEPVGNVLFSPICLSTSLSLAQVGAKGDTANEIGQVLHFDNVKDVPFGF
          MDALRLANSAFAVDLFKQLCEKEPVGNVLFSPICLSTSLSLAQVGAKGDTANEIGQVLHFDNVKDVPFG.
Retrocopy MDALRLANSAFAVDLFKQLCEKEPVGNVLFSPICLSTSLSLAQVGAKGDTANEIGQVLHFDNVKDVPFGY

Parental  QTVTSDVNKLSSFYSLKLIKRLYVDKSLNPSTEFISSTKRPYAKELETVDFKDKLEETKGQINSSIKDLT
          QTVTSDVNKLSSFYSLK.IKRLYVDKSLNPSTEFISSTKRPYAKELETVDFKDKLEETKGQINSSIKDLT
Retrocopy QTVTSDVNKLSSFYSLKPIKRLYVDKSLNPSTEFISSTKRPYAKELETVDFKDKLEETKGQINSSIKDLT

Parental  DGHFENILSDNSVNDQTKILVVNAAYFVGKWMKKFPESETKECPFRVSKTDAKPVQMMNMEATFCMGNID
          DGHFENILSDNSVNDQTKILVVNAAYFVGKWMKKFPESETKECPFRVSKTDAKPVQMMNMEATFCMGNID
Retrocopy DGHFENILSDNSVNDQTKILVVNAAYFVGKWMKKFPESETKECPFRVSKTDAKPVQMMNMEATFCMGNID

Parental  DINCKIIELPFQNKHLSMLILLPKDVEDESTGLEKIEKQLNSETLLQWTNPSTMANAKVKLSLPKFKVEK
          DINCKIIELPFQNKHLSMLILLPKDVEDES.GLEKIEKQLNSETL.QWTNPSTMANAKVKLSLPKFKVEK
Retrocopy DINCKIIELPFQNKHLSMLILLPKDVEDESMGLEKIEKQLNSETLFQWTNPSTMANAKVKLSLPKFKVEK

Parental  IIDPKSSLENLGLKNTFNEDTSDFSGMSETKGVALSNVIHRACLEINEDGGESIEVPGSRILQHKDEFNA
          IIDPKSSLENLGLKNTFNEDTSDFSGMSETKGVALSNVIHRACLEINEDGGESIEVPGSRILQHKDEFNA
Retrocopy IIDPKSSLENLGLKNTFNEDTSDFSGMSETKGVALSNVIHRACLEINEDGGESIEVPGSRILQHKDEFNA

Parental  DHPFIYIIRHNKTRNIIFFGKFCTP
          DHPFIYIIRHNKTRNIIFFGKFCTP
Retrocopy DHPFIYIIRHNKTRNIIFFGKFCTP

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_115 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_115 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013882	1 retrocopy	retro_cpor_1174,
Rattus norvegicus	ENSRNOG00000002640	1 retrocopy	retro_rnor_2400,
Ictidomys tridecemlineatus	ENSSTOG00000007438	1 retrocopy	retro_itri_115 ,