RetrogeneDB ID: retro_itri_138

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH398297.1:48..1368(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023441
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000014692
• Aliases: None
• Description: None

Sequence

>retro_itri_138
ATGAGCTACGGTCTCCAGCTGACCTTCGTGTGTCTGAGCCTCTTGGCTCCAAGGATGTGCGTCCAGGGGAACCAGTTCAA
CATCGAGGTCAGAAGTGACAAGCTCTCCCTGCCTGGCTTTGAGAACCTCACAGCAGGATATAACAAATTTCTCAGGCCCA
ACTTTGGTGGAGAACCAGTTCAGATAGCACTGACTCTGGACATCGCAAGCATCTCTAGTATTTCCGAGAGTAACATGGAC
TACACGGCCACCATATACCTCCAACAGCGCTGGACAGACCCGCGGCTGGTGTTTGAAGGCAACAAGAGCTTCACTCTGGA
CGCCCGCCTGGTGGAGTTCTTCTGGGTGCCTGACACCTACATCGTGGAGTCCAGGAAGTCCTTCCTCCACGAAGTCACTG
TGGGAAACAGACTCATCCGCCTCTTCTCCAACGGCACAGTCCTGTATGCGCTCAGAATCACAACGACTGTGGCATGCAAC
ATGGACCTGTCCAAGTACCCCATGGACACGCAGACCTGCAAGCTGCAGCTGGAGAGCTGGGGCTATGATGGAAATGACGT
GGTGTTCACCTGGCTGAGAGGGAATGATTCCGTGCGAGGGCTGGAAAACCTGCGACTTGCTCAGTATACCATACAACGCT
ACTTCACCTTAGTCACCAGGTCCCAGCAGGAGACAGGAAATTACTCCCGGTTGGTCTTGCAATTTGAGCTGCGGAGGAAT
GTCCTGTATTTCATTCTGGAAACCTATGTTCTCTCCACTTTCCTGGTGGTGCTGTCCTGGGTTTCATTTTGGATCTCCCT
AGATTCTGTCCCTGCAAGAACCTGCATCGGAGTGACCACTGTGTTACCAATGACCACACTGATGATCGGGTCCCCCATGT
CTCTTCCCAACACCAACTGCTTCATCAAAGCCATCAACGTGTACCTGGGGATCTGCTTTAGCTTTGTGTTTGGGGCCTTG
GTGGAGTACGCTGTTGCTCACTACAGCTCCCTGCAACAGATGGAAGCCAAGGACAGGGGGACGGCGAAGGAGGTGGAAGA
AGTCAACATCACTAACATCATCAACAGCTCCCTCTCCAGCTTTAAGCGGAAGATCAGCTTTGCCACCATTGAAATCTCGG
GTGACAATGTTGACTACAGCAACATGACAATGAAAACCAGCGACAAGTTCAAGTTCATCTTCCGAGAAAAGATGGGCAGG
ATTGTGGATTATTTCACAATTCAAAACCCCAGCAATGTTGATCGATATTCCAAACTACTGTTCCCTTTGGTTTTTATGCT
AGCCAATGTTTTCTACTGGGCATACTACCTGTACTTCTGA

Alignment

ORF - retro_itri_138 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYGLQLTFVCLSLLAPRMCVQGNQFNIEVRRSDKLSLPGFENLTAGYNKFLRPNFGGEPVQIALTLDIA
          MSYGLQLTFVCLSLLAPRMCVQGNQFNIEVR.SDKLSLPGFENLTAGYNKFLRPNFGGEPVQIALTLDIA
Retrocopy MSYGLQLTFVCLSLLAPRMCVQGNQFNIEVR-SDKLSLPGFENLTAGYNKFLRPNFGGEPVQIALTLDIA

Parental  SISSISESNMDYTATIYLRQRWTDPRLVFEGNKSFTLDARLVEFLWVPDTYIVESKKSFLHEVTVGNRLI
          SISSISESNMDYTATIYL.QRWTDPRLVFEGNKSFTLDARLVEF.WVPDTYIVES.KSFLHEVTVGNRLI
Retrocopy SISSISESNMDYTATIYLQQRWTDPRLVFEGNKSFTLDARLVEFFWVPDTYIVESRKSFLHEVTVGNRLI

Parental  RLFSNGTVLYALRITTTVACNMDLSKYPMDTQTCKLQLESWGYDGNDVEFTWLRGNDSVRGLENLRLAQY
          RLFSNGTVLYALRITTTVACNMDLSKYPMDTQTCKLQLESWGYDGNDV.FTWLRGNDSVRGLENLRLAQY
Retrocopy RLFSNGTVLYALRITTTVACNMDLSKYPMDTQTCKLQLESWGYDGNDVVFTWLRGNDSVRGLENLRLAQY

Parental  TIQRYFTLVTRSQQETGNYTRLVLHFELRRNVLYFILETYVPSTFLVVLSWVSFWISLDSVPARTCIGVT
          TIQRYFTLVTRSQQETGNY.RLVL.FELRRNVLYFILETYV.STFLVVLSWVSFWISLDSVPARTCIGVT
Retrocopy TIQRYFTLVTRSQQETGNYSRLVLQFELRRNVLYFILETYVLSTFLVVLSWVSFWISLDSVPARTCIGVT

Parental  TVLSMTTLMIGSRTSLPNTNCFIKAIDVYLGICFSFVFGALVEYAIAHYSSLQQMEAKDRGTAKEVEEVN
          TVL.MTTLMIGS..SLPNTNCFIKAI.VYLGICFSFVFGALVEYA.AHYSSLQQMEAKDRGTAKEVEEVN
Retrocopy TVLPMTTLMIGSPMSLPNTNCFIKAINVYLGICFSFVFGALVEYAVAHYSSLQQMEAKDRGTAKEVEEVN

Parental  ITNIINSSLSSFKRKISFATIEISGDNVDYSNMTMKTSDKFKFVFREKMGRIVDYFTIQNPSNVDRYSKL
          ITNIINSSLSSFKRKISFATIEISGDNVDYSNMTMKTSDKFKF.FREKMGRIVDYFTIQNPSNVDRYSKL
Retrocopy ITNIINSSLSSFKRKISFATIEISGDNVDYSNMTMKTSDKFKFIFREKMGRIVDYFTIQNPSNVDRYSKL

Parental  LFPLVFMLANVFYWAYYLYF
          LFPLVFMLANVFYWAYYLYF
Retrocopy LFPLVFMLANVFYWAYYLYF

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_138 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_138 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	ENSSTOG00000014692	1 retrocopy	retro_itri_138 ,