RetrogeneDB ID: retro_itri_120

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH395699.1:272..1172(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025218
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015170
• Aliases: None
• Description: None

Sequence

>retro_itri_120
ATGGAACATTTTGATGCATCACTCAGTACCTATTTCAAGGTCTTGCTGGGCCCCCGAGATACCAGAGTAAAAGGATGGTT
TCTTCTGGACAATTACATACCTACCTTTGTCTGCACTGTCATTTATTTACTAATTGTATGGTTAGGACCAAAATACATGA
AGAAAAAACAGCCATTCTCTTGCCGGGGAATCTTAGTGGTGTATAACCTTGGACTCACGTTGCTGTCTCTCTACATGTTC
TGTGAGTTGGTGACAGGAGTATGGCAAGGCAGCTACAACTTCTTTTGTCAGGGCACATGCAGTGCGGGAGAATCAGACAT
GAAGATCATCCGTGTCCTTTGGTGGTATTACTTCTCTAAACTCATAGAATTCATGGACACATTTTTCTTCATCCTGTGCA
AGAACAACCATCAGATCACAGTCCTGCACGACTACCACCATGCCACCATGTTCAACATCTGGTGGTTTGTGATGAACTGG
GTACCATGTGGCCACTCTTATTTCGGTGCCACACTTAATAGCTTCATCCATGTCCTCATGTACTCGTACTATGGCTTGTC
ATCTGTACCTTCCATGCGCCCATACCTCTGGTGGAAGAAGTACATCACTCAGGGACAGCTGGTTCAGTTTGTGCTGACAA
TCATTCAGACCAGCTGTGGGGTCATCTGGCCATGTGTGTTCCCTCTTGGTTGGCTATATTTCCAGATTGGATACATGATA
TCCCTGATTGCTCTCTTCACAAACTTTTACATTGAGACTTACAACATGAAAGGAGCCTCTCGGAGGAGAGGCTACCAAAA
GGACCACCAGAATGGATCTGTGACTGCTGTGAATGAACACACCAACAGCTTTTCTTCCCTGGAAAACACAGCGAAGCCAA
GGAAGCAACGGAAGGATTGA

Alignment

ORF - retro_itri_120 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEHFDASLSTYFKALLGPRDTRVKGWFLLDNYIPTFVCTVIYLLIVWLGPKYMKNKQPFSCRGILVVYNL
          MEHFDASLSTYFK.LLGPRDTRVKGWFLLDNYIPTFVCTVIYLLIVWLGPKYMK.KQPFSCRGILVVYNL
Retrocopy MEHFDASLSTYFKVLLGPRDTRVKGWFLLDNYIPTFVCTVIYLLIVWLGPKYMKKKQPFSCRGILVVYNL

Parental  GLTLLSLYMFCELVTGVWQGSYNFFCQGTRSAGESDMKIIRVLWWYYFSKLIEFMDTFFFILRKNNHQIT
          GLTLLSLYMFCELVTGVWQGSYNFFCQGT.SAGESDMKIIRVLWWYYFSKLIEFMDTFFFIL.KNNHQIT
Retrocopy GLTLLSLYMFCELVTGVWQGSYNFFCQGTCSAGESDMKIIRVLWWYYFSKLIEFMDTFFFILCKNNHQIT

Parental  VLHVYHHATMFNIWWFVMNWVPCGHSYFGATLNSFIHVLMYSYYGLSSVPSMRPYLWWKKYITQGQLVQF
          VLH.YHHATMFNIWWFVMNWVPCGHSYFGATLNSFIHVLMYSYYGLSSVPSMRPYLWWKKYITQGQLVQF
Retrocopy VLHDYHHATMFNIWWFVMNWVPCGHSYFGATLNSFIHVLMYSYYGLSSVPSMRPYLWWKKYITQGQLVQF

Parental  VLTIIQTSCGVIWPCAFPLGWLYFQIGYMISLIALFTNFYIETYNKKGASRRRGYQKDHQNGSVTAVNGH
          VLTIIQTSCGVIWPC.FPLGWLYFQIGYMISLIALFTNFYIETYN.KGASRRRGYQKDHQNGSVTAVN.H
Retrocopy VLTIIQTSCGVIWPCVFPLGWLYFQIGYMISLIALFTNFYIETYNMKGASRRRGYQKDHQNGSVTAVNEH

Parental  TNSFSSLENNAKPRKQRKD
          TNSFSSLEN.AKPRKQRKD
Retrocopy TNSFSSLENTAKPRKQRKD

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_120 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_120 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011119	1 retrocopy	retro_cjac_1568,
Ictidomys tridecemlineatus	ENSSTOG00000015170	2 retrocopies	retro_itri_120 , retro_itri_143,
Tarsius syrichta	ENSTSYG00000000707	1 retrocopy	retro_tsyr_229,