RetrogeneDB ID: retro_itri_147

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:26495204..26495990(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021862
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MAPRE3
• Ensembl ID: ENSSTOG00000015500
• Aliases: None
• Description: microtubule-associated protein, RP/EB family, member 3 [Source:HGNC Symbol;Acc:6892]

Sequence

>retro_itri_147
ATGGCAGTGACCCGGACCGACCTAAGTCGACTGGACATGCTGGCCTGGATCAATGAGTCTCTGCAGCTGAATGTGACAAA
GATCAAACAGTTGTGCTCAGGGGCTGCCTATTGTCAGTTTATGGACATGCTATTCCCTGGCTCCATTGCCTTGAAGAAAG
TGAAATTCCAAGCCAAGCTAGAACATGAATATATCCAGAACCTCAAAATACTGCAAGCAGGTTTTAAGAAGATGGGAGTT
GACAAAATAATTCCTGTGGATAAATTAGTGAAAGGAAAATTTCAGGACAATTTTGAGTTCGCGCAGTGGTTCAAGAAATT
TTTTGATGCAAACTATAAAGGAGAAGACCATGACCCTGTAGCTGCCAGACAAGGTCGAGAAACTGCAGGCACTCCTTCCC
TGGTTGCTGCAGCTCCCAACAAACAGAAGAGACCCCTCCACTCCAGCAGTGCGGCTCCCCAGAGAACCGTTTCAACACGG
AAAACTACCGCAACTCCCAAGGTCGCCCCAGGGGTGGTGCGAAAGAATCCTGGTATGGGAGACGGCGACAGCAAAGCAGC
CGAATGGATGCAGCGGGTCAACGTATTGAAGCATACTGTAGAAGGTTTGGAGAAAGAGAGAGATTTCTACTTCGGAAAGC
TGAGGAACATTGAATTGATTTGCCAGGAGAATGAGGGGGAAAGTGACCCCATACTGCAGAGGATTGTAGACATTCTCTAT
GCCAGAGACCAAGGCTTTGTGACATCCAATGAAGGGGCCCCAAAGGAGGAACAAGAAGAGTTTTAA

Alignment

ORF - retro_itri_147 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.99 %
• Parental protein coverage: 55.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVTSENLSRHDMLAWVNDSLHLNYTKIEQLCSGAAYCQFMDMLFPGCVHLRKVKFQAKLEHEYIHNFKVL
          .VT...LSR.DMLAW.N.SL.LN.TKI.QLCSGAAYCQFMDMLFPG...L.KVKFQAKLEHEYI.N.K.L
Retrocopy AVTRTDLSRLDMLAWINESLQLNVTKIKQLCSGAAYCQFMDMLFPGSIALKKVKFQAKLEHEYIQNLKIL

Parental  QAAFKKMGVDKIIPVEKLVKGKFQDNFEFIQWFKKFFDANYDGKDYNPLLARQGQDVAPPPNPGDQIFNK
          QA.FKKMGVDKIIPV.KLVKGKFQDNFEF.QWFKKFFDANY.G.D..P..ARQG...A..P.......NK
Retrocopy QAGFKKMGVDKIIPVDKLVKGKFQDNFEFAQWFKKFFDANYKGEDHDPVAARQGRETAGTPSLVAAAPNK

Parental  SKKLI--GTAVPQRTSPT
          .K.......A.PQRT..T
Retrocopy QKRPLHSSSAAPQRTVST

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_147 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_147 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016515	1 retrocopy	retro_ecab_40,
Ictidomys tridecemlineatus	ENSSTOG00000015500	1 retrocopy	retro_itri_147 ,
Tupaia belangeri	ENSTBEG00000013617	1 retrocopy	retro_tbel_2390,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,